1-76714005-T-C

Variant names:

• chr1-76714005-T-C
• rs664576

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 0.682 in 151,592 control chromosomes in the GnomAD database, including 35,773 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 0.68 (35773 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.769 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: 0.682 AC: 103304 AN: 151474 Hom.: 35772 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.682 AC: 103332 AN: 151592 Hom.: 35773 Cov.: 31 AF XY: 0.676 AC XY: 50111 AN XY: 74082

African (AFR) AF: 0.575 AC: 23804 AN: 41398

American (AMR) AF: 0.781 AC: 11869 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2482 AN: 3460

East Asian (EAS) AF: 0.539 AC: 2775 AN: 5148

South Asian (SAS) AF: 0.545 AC: 2608 AN: 4786

European-Finnish (FIN) AF: 0.708 AC: 7456 AN: 10526

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 49966 AN: 67762

Other (OTH) AF: 0.690 AC: 1451 AN: 2104

Alfa AF: 0.733 Hom.: 64201

Bravo AF: 0.690

Asia WGS AF: 0.570 AC: 1975 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.61
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs664576; hg19: chr1-77179690;