rs67418890

chr1-161571067-T-Achr1-161571067-T-C

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 0.101 in 140,928 control chromosomes in the GnomAD database, including 1,941 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 0.10 (1941 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 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: 0.101 AC: 14274 AN: 140816 Hom.: 1940 Cov.: 32

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.0913

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.000818

Gnomad SAS AF: 0.0709

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.101 AC: 14268 AN: 140928 Hom.: 1941 Cov.: 32 AF XY: 0.101 AC XY: 6928 AN XY: 68772

Gnomad4 AFR AF: 0.0267

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.000820

Gnomad4 SAS AF: 0.0705

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0268 Hom.: 46

Asia WGS AF: 0.0280 AC: 98 AN: 3350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.2
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs67418890; hg19: chr1-161540857;