1-65116340-A-T

Variant names:

• chr1-65116340-A-T
• rs7555622

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 0.758 in 152,168 control chromosomes in the GnomAD database, including 44,116 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 0.76 (44116 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115353 AN: 152050 Hom.: 44113 Cov.: 33

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.758 AC: 115404 AN: 152168 Hom.: 44116 Cov.: 33 AF XY: 0.755 AC XY: 56150 AN XY: 74386

African (AFR) AF: 0.683 AC: 28332 AN: 41486

American (AMR) AF: 0.691 AC: 10566 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2859 AN: 3472

East Asian (EAS) AF: 0.633 AC: 3280 AN: 5180

South Asian (SAS) AF: 0.788 AC: 3805 AN: 4828

European-Finnish (FIN) AF: 0.777 AC: 8228 AN: 10588

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.820 AC: 55785 AN: 68010

Other (OTH) AF: 0.760 AC: 1606 AN: 2114

Alfa AF: 0.787 Hom.: 5586

Bravo AF: 0.745

Asia WGS AF: 0.697 AC: 2425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.29
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7555622; hg19: chr1-65582023; COSMIC: COSV59949828;