rs1370051

Variant names:

• chr13-57934694-G-A
• rs1370051
• ENST00000823953.1:n.458+8061G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-57934694-G-A
• chr13-57934694-G-C
• chr13-57934694-G-T

Variant summary

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

The ENST00000823953.1(ENSG00000307112):​n.458+8061G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.865 in 151,990 control chromosomes in the GnomAD database, including 59,655 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 0.86 (59655 hom., cov: 32)
• Consequence: ENSG00000307112 ENST00000823953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 0 publications found

Genes affected

ENSG00000307112 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307112	ENST00000823953.1	n.458+8061G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.865 AC: 131360 AN: 151872 Hom.: 59635 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.865 AC: 131423 AN: 151990 Hom.: 59655 Cov.: 32 AF XY: 0.868 AC XY: 64434 AN XY: 74274

African (AFR) AF: 0.557 AC: 23071 AN: 41396

American (AMR) AF: 0.949 AC: 14453 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3469 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4440 AN: 5166

South Asian (SAS) AF: 0.965 AC: 4649 AN: 4820

European-Finnish (FIN) AF: 0.981 AC: 10420 AN: 10624

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67816 AN: 67968

Other (OTH) AF: 0.906 AC: 1907 AN: 2106

Alfa AF: 0.906 Hom.: 8371

Bravo AF: 0.848

Asia WGS AF: 0.885 AC: 3077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.43
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1370051; hg19: chr13-58508828;