rs12071951

Variant names:

• chr1-96648359-T-G
• rs12071951

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 0.263 in 152,074 control chromosomes in the GnomAD database, including 6,553 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 0.26 (6553 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 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: 0.263 AC: 40025 AN: 151956 Hom.: 6539 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.263 AC: 40066 AN: 152074 Hom.: 6553 Cov.: 32 AF XY: 0.261 AC XY: 19397 AN XY: 74326

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.245

Alfa AF: 0.201 Hom.: 3038

Bravo AF: 0.270

Asia WGS AF: 0.210 AC: 731 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12071951; hg19: chr1-97113915; COSMIC: COSV59976173;