rs951821

Variant names:

• chr12-28666573-G-A
• rs951821

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 0.346 in 151,710 control chromosomes in the GnomAD database, including 9,527 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 0.35 (9527 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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: 0.346 AC: 52473 AN: 151592 Hom.: 9530 Cov.: 31

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.346 AC: 52490 AN: 151710 Hom.: 9527 Cov.: 31 AF XY: 0.342 AC XY: 25379 AN XY: 74144

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.330

Alfa AF: 0.342 Hom.: 4869

Bravo AF: 0.339

Asia WGS AF: 0.223 AC: 777 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs951821; hg19: chr12-28819506;