rs927724

Positions:

• chr1-196205660-G-A
• chr1-196205660-G-T

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 0.893 in 152,096 control chromosomes in the GnomAD database, including 60,756 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 0.89 (60756 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 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: 0.893 AC: 135770 AN: 151982 Hom.: 60688 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.893 AC: 135894 AN: 152096 Hom.: 60756 Cov.: 31 AF XY: 0.893 AC XY: 66421 AN XY: 74354

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.901

Alfa AF: 0.884 Hom.: 64108

Bravo AF: 0.897

Asia WGS AF: 0.874 AC: 3024 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.51
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs927724; hg19: chr1-196174790;