rs676614

Variant names:

• chr1-35641909-C-A
• rs676614

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.665 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

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.584

Gnomad4 ASJ exome AF: 0.868

Gnomad4 EAS exome AF: 0.191

Gnomad4 SAS exome AF: 0.702

Gnomad4 FIN exome AF: 0.864

Gnomad4 NFE exome AF: 0.909

Gnomad4 OTH exome AF: 0.781

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

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.694

Alfa AF: 0.844 Hom.: 37318

Bravo AF: 0.626

Asia WGS AF: 0.460 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.65
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

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