rs951821

Positions:

• chr12-28666573-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;