rs1358716

Variant names:

• chr6-139124867-A-G
• rs1358716

Variant summary

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

The variant allele was found at a frequency of 0.561 in 151,902 control chromosomes in the GnomAD database, including 24,908 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 0.56 (24908 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 4 publications found

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 = 0.605 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

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85139 AN: 151784 Hom.: 24900 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.0405

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.561 AC: 85185 AN: 151902 Hom.: 24908 Cov.: 31 AF XY: 0.551 AC XY: 40864 AN XY: 74208

African (AFR) AF: 0.611 AC: 25310 AN: 41426

American (AMR) AF: 0.515 AC: 7852 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2178 AN: 3466

East Asian (EAS) AF: 0.0406 AC: 210 AN: 5172

South Asian (SAS) AF: 0.396 AC: 1909 AN: 4818

European-Finnish (FIN) AF: 0.555 AC: 5840 AN: 10530

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39927 AN: 67928

Other (OTH) AF: 0.581 AC: 1224 AN: 2108

Alfa AF: 0.586 Hom.: 29417

Bravo AF: 0.562

Asia WGS AF: 0.246 AC: 859 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	0.16
DANN	Benign	0.46
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1358716; hg19: chr6-139446004; COSMIC: COSV60286487;