rs56993779

Variant names:

• chr8-86214405-TCCGACATC-T
• rs56993779
• NM_138817.3:c.1413_*7delGATGTCGG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 2P and 10B. PM4 BP6_Moderate BA1

The NM_138817.3(SLC7A13):​c.1413_*7delGATGTCGG​(p.Ter471fs) variant causes a frameshift, stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 1,572,080 control chromosomes in the GnomAD database, including 20,645 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.13 (1705 hom., cov: 30)
  • Exomes 𝑓: 0.15 (18940 hom.)
• Consequence: SLC7A13 NM_138817.3 frameshift, stop_lost
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.83
• Publications: 8 publications found

Genes affected

SLC7A13 (HGNC:23092): (solute carrier family 7 member 13) Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in L-cystine transport; L-glutamate transmembrane transport; and aspartate transmembrane transport. Predicted to be integral component of membrane. Predicted to be active in apical plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• PM4: Stoplost variant in NM_138817.3
• BP6: Variant 8-86214405-TCCGACATC-T is Benign according to our data. Variant chr8-86214405-TCCGACATC-T is described in ClinVar as Benign. ClinVar VariationId is 1620765.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A13	NM_138817.3	c.1413_*7delGATGTCGG	p.Ter471fs	frameshift_variant, stop_lost	Exon 4 of 4	ENST00000297524.8	NP_620172.2
SLC7A13	NM_138817.3	c.1413_*7delGATGTCGG		3_prime_UTR_variant	Exon 4 of 4	ENST00000297524.8	NP_620172.2
SLC7A13	XM_011516867.3	c.1386_*7delGATGTCGG	p.Ter462fs	frameshift_variant, stop_lost	Exon 4 of 4		XP_011515169.1
SLC7A13	XM_011516867.3	c.1386_*7delGATGTCGG		3_prime_UTR_variant	Exon 4 of 4		XP_011515169.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC7A13	ENST00000297524.8	c.1413_*7delGATGTCGG	p.Ter471fs	frameshift_variant, stop_lost	Exon 4 of 4	1	NM_138817.3	ENSP00000297524.3
SLC7A13	ENST00000297524.8	c.1413_*7delGATGTCGG		3_prime_UTR_variant	Exon 4 of 4	1	NM_138817.3	ENSP00000297524.3
SLC7A13	ENST00000419776.2	c.*212_*219delGATGTCGG		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000410982.2

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19557 AN: 151998 Hom.: 1700 Cov.: 30

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.149

GnomAD2 exomes AF: 0.181 AC: 42497 AN: 234406 AF XY: 0.187

Gnomad AFR exome AF: 0.0555

Gnomad AMR exome AF: 0.236

Gnomad ASJ exome AF: 0.194

Gnomad EAS exome AF: 0.320

Gnomad FIN exome AF: 0.116

Gnomad NFE exome AF: 0.134

Gnomad OTH exome AF: 0.170

GnomAD4 exome AF: 0.150 AC: 212309 AN: 1419964 Hom.: 18940 AF XY: 0.155 AC XY: 109814 AN XY: 707404

African (AFR) AF: 0.0519 AC: 1664 AN: 32054

American (AMR) AF: 0.229 AC: 9628 AN: 42068

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 4893 AN: 25382

East Asian (EAS) AF: 0.318 AC: 12473 AN: 39226

South Asian (SAS) AF: 0.318 AC: 26728 AN: 84124

European-Finnish (FIN) AF: 0.118 AC: 5727 AN: 48344

Middle Eastern (MID) AF: 0.266 AC: 1502 AN: 5648

European-Non Finnish (NFE) AF: 0.129 AC: 140310 AN: 1084262

Other (OTH) AF: 0.159 AC: 9384 AN: 58856

GnomAD4 genome AF: 0.129 AC: 19574 AN: 152116 Hom.: 1705 Cov.: 30 AF XY: 0.132 AC XY: 9837 AN XY: 74348

African (AFR) AF: 0.0561 AC: 2329 AN: 41546

American (AMR) AF: 0.176 AC: 2683 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3470

East Asian (EAS) AF: 0.321 AC: 1652 AN: 5140

South Asian (SAS) AF: 0.318 AC: 1534 AN: 4820

European-Finnish (FIN) AF: 0.114 AC: 1206 AN: 10590

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.132 AC: 8988 AN: 67982

Other (OTH) AF: 0.150 AC: 317 AN: 2112

Alfa AF: 0.137 Hom.: 326

Bravo AF: 0.128

Asia WGS AF: 0.322 AC: 1119 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs56993779; hg19: chr8-87226634;