1-79818003-T-G

Variant names:

• chr1-79818003-T-G
• rs10493644

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 0.547 in 151,888 control chromosomes in the GnomAD database, including 23,005 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 0.55 (23005 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.609 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: 0.547 AC: 82998 AN: 151770 Hom.: 22990 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.547 AC: 83053 AN: 151888 Hom.: 23005 Cov.: 31 AF XY: 0.549 AC XY: 40763 AN XY: 74236

African (AFR) AF: 0.508 AC: 21047 AN: 41418

American (AMR) AF: 0.619 AC: 9456 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2364 AN: 3468

East Asian (EAS) AF: 0.328 AC: 1684 AN: 5132

South Asian (SAS) AF: 0.533 AC: 2571 AN: 4820

European-Finnish (FIN) AF: 0.610 AC: 6431 AN: 10546

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37708 AN: 67916

Other (OTH) AF: 0.551 AC: 1165 AN: 2114

Alfa AF: 0.554 Hom.: 12222

Bravo AF: 0.544

Asia WGS AF: 0.431 AC: 1497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.73
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs10493644; hg19: chr1-80283688; COSMIC: COSV59960585;