rs727955

chr1-195042636-C-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 0.668 in 151,856 control chromosomes in the GnomAD database, including 34,267 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 0.67 (34267 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 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: 0.668 AC: 101350 AN: 151738 Hom.: 34243 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.668 AC: 101420 AN: 151856 Hom.: 34267 Cov.: 31 AF XY: 0.671 AC XY: 49798 AN XY: 74202

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.689

Alfa AF: 0.685 Hom.: 5247

Bravo AF: 0.659

Asia WGS AF: 0.589 AC: 2047 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727955; hg19: chr1-195011766; COSMIC: COSV60009327;