rs1328950

Variant names:

• chr13-31442143-A-G
• rs1328950
• ENST00000843719.1:n.220-24692A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-31442143-A-G
• chr13-31442143-A-T

Variant summary

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

The ENST00000843719.1(ENSG00000278305):​n.220-24692A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,148 control chromosomes in the GnomAD database, including 1,601 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 0.14 (1601 hom., cov: 32)
• Consequence: ENSG00000278305 ENST00000843719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 2 publications found

Genes affected

ENSG00000278305 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370150	XR_001749806.1	n.359+963A>G		intron_variant	Intron 1 of 3
LOC105370150	XR_941829.1	n.231+963A>G		intron_variant	Intron 3 of 5
LOC105370150	XR_941830.1	n.233+963A>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000278305	ENST00000843719.1	n.220-24692A>G		intron_variant	Intron 1 of 3
ENSG00000278305	ENST00000843720.1	n.487+963A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21505 AN: 152028 Hom.: 1600 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.141 AC: 21520 AN: 152148 Hom.: 1601 Cov.: 32 AF XY: 0.145 AC XY: 10801 AN XY: 74386

African (AFR) AF: 0.125 AC: 5180 AN: 41522

American (AMR) AF: 0.143 AC: 2185 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 470 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1386 AN: 5138

South Asian (SAS) AF: 0.264 AC: 1271 AN: 4816

European-Finnish (FIN) AF: 0.148 AC: 1565 AN: 10600

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9121 AN: 67996

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.0615 Hom.: 68

Bravo AF: 0.137

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.78
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1328950; hg19: chr13-32016280;