rs953197

Variant names:

• chr1-84075603-T-C
• rs953197

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 0.374 in 151,992 control chromosomes in the GnomAD database, including 11,926 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 0.37 (11926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 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: 0.374 AC: 56767 AN: 151874 Hom.: 11922 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.374 AC: 56778 AN: 151992 Hom.: 11926 Cov.: 32 AF XY: 0.370 AC XY: 27530 AN XY: 74314

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.384

Alfa AF: 0.428 Hom.: 2778

Bravo AF: 0.359

Asia WGS AF: 0.284 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs953197; hg19: chr1-84541286; COSMIC: COSV65771781;