1-79773713-C-T

Variant names:

• chr1-79773713-C-T
• rs5008948

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 0.644 in 151,992 control chromosomes in the GnomAD database, including 32,396 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 0.64 (32396 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97764 AN: 151874 Hom.: 32380 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.644 AC: 97816 AN: 151992 Hom.: 32396 Cov.: 31 AF XY: 0.646 AC XY: 47990 AN XY: 74292

African (AFR) AF: 0.505 AC: 20927 AN: 41422

American (AMR) AF: 0.698 AC: 10647 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2458 AN: 3468

East Asian (EAS) AF: 0.377 AC: 1948 AN: 5172

South Asian (SAS) AF: 0.610 AC: 2940 AN: 4820

European-Finnish (FIN) AF: 0.786 AC: 8320 AN: 10590

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48509 AN: 67956

Other (OTH) AF: 0.645 AC: 1360 AN: 2108

Alfa AF: 0.687 Hom.: 148888

Bravo AF: 0.629

Asia WGS AF: 0.490 AC: 1703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.25
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs5008948; hg19: chr1-80239398;