rs727955

Variant names:

• chr1-195042636-C-T
• rs727955

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.576 AC: 23818 AN: 41378

American (AMR) AF: 0.685 AC: 10429 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2484 AN: 3466

East Asian (EAS) AF: 0.562 AC: 2897 AN: 5158

South Asian (SAS) AF: 0.710 AC: 3416 AN: 4814

European-Finnish (FIN) AF: 0.780 AC: 8229 AN: 10550

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47956 AN: 67946

Other (OTH) AF: 0.689 AC: 1453 AN: 2108

Alfa AF: 0.681 Hom.: 5370

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
PhyloP100		0.057

Splicing

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

Other links and lift over

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