19-33223022-C-T

Variant names:

• chr19-33223022-C-T
• rs8106493
• NM_019849.3:c.151+2531G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019849.3(SLC7A10):​c.151+2531G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,030 control chromosomes in the GnomAD database, including 3,037 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3037 hom., cov: 31)
• Consequence: SLC7A10 NM_019849.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572
• Publications: 8 publications found

Genes affected

SLC7A10 (HGNC:11058): (solute carrier family 7 member 10) SLC7A10, in association with 4F2HC (SLC3A2; MIM 158070), mediates high-affinity transport of D-serine and several other neutral amino acids (Nakauchi et al., 2000 [PubMed 10863037]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A10	NM_019849.3	c.151+2531G>A		intron_variant	Intron 1 of 10	ENST00000253188.8	NP_062823.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC7A10	ENST00000253188.8	c.151+2531G>A		intron_variant	Intron 1 of 10	1	NM_019849.3	ENSP00000253188.2
SLC7A10	ENST00000592596.1	n.151+2531G>A		intron_variant	Intron 1 of 3	1		ENSP00000466410.1
SLC7A10	ENST00000587064.5	n.151+2531G>A		intron_variant	Intron 1 of 4	3		ENSP00000466876.1
SLC7A10	ENST00000590036.5	n.151+2531G>A		intron_variant	Intron 1 of 9	5		ENSP00000465421.1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29794 AN: 151912 Hom.: 3037 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.205

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.196 AC: 29801 AN: 152030 Hom.: 3037 Cov.: 31 AF XY: 0.193 AC XY: 14361 AN XY: 74338

African (AFR) AF: 0.216 AC: 8973 AN: 41464

American (AMR) AF: 0.179 AC: 2734 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3468

East Asian (EAS) AF: 0.128 AC: 664 AN: 5170

South Asian (SAS) AF: 0.192 AC: 927 AN: 4818

European-Finnish (FIN) AF: 0.131 AC: 1386 AN: 10570

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13669 AN: 67952

Other (OTH) AF: 0.203 AC: 427 AN: 2108

Alfa AF: 0.203 Hom.: 12769

Bravo AF: 0.200

Asia WGS AF: 0.139 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.62
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs8106493; hg19: chr19-33713928;