rs676614

chr1-35641909-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;