rs676614

Variant names:

• chr1-35641909-C-A
• rs676614

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 0.695 in 183,736 control chromosomes in the GnomAD database, including 51,399 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 0.66 (39622 hom., cov: 30)
  • Exomes 𝑓: 0.84 (11777 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.894 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: 0.665 AC: 101014 AN: 151826 Hom.: 39627 Cov.: 30

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.694

GnomAD4 exome AF: 0.842 AC: 26770 AN: 31792 Hom.: 11777 AF XY: 0.839 AC XY: 13639 AN XY: 16250

African (AFR) AF: 0.206 AC: 143 AN: 694

American (AMR) AF: 0.584 AC: 816 AN: 1398

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 264 AN: 304

East Asian (EAS) AF: 0.191 AC: 137 AN: 718

South Asian (SAS) AF: 0.702 AC: 1714 AN: 2440

European-Finnish (FIN) AF: 0.864 AC: 178 AN: 206

Middle Eastern (MID) AF: 0.845 AC: 71 AN: 84

European-Non Finnish (NFE) AF: 0.909 AC: 22586 AN: 24846

Other (OTH) AF: 0.781 AC: 861 AN: 1102

GnomAD4 genome AF: 0.665 AC: 101003 AN: 151944 Hom.: 39622 Cov.: 30 AF XY: 0.660 AC XY: 48969 AN XY: 74248

African (AFR) AF: 0.272 AC: 11275 AN: 41384

American (AMR) AF: 0.622 AC: 9496 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2914 AN: 3472

East Asian (EAS) AF: 0.223 AC: 1151 AN: 5166

South Asian (SAS) AF: 0.678 AC: 3267 AN: 4820

European-Finnish (FIN) AF: 0.861 AC: 9078 AN: 10538

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61205 AN: 67972

Other (OTH) AF: 0.694 AC: 1465 AN: 2110

Alfa AF: 0.816 Hom.: 143574

Bravo AF: 0.626

Asia WGS AF: 0.460 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.65
DANN	Benign	0.50
PhyloP100		-1.1
PromoterAI		-0.029	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs676614; hg19: chr1-36107510; COSMIC: COSV64698572;