12-52004967-A-G

Variant names:

• chr12-52004967-A-G
• rs7955401

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 0.947 in 152,074 control chromosomes in the GnomAD database, including 68,223 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 0.95 (68223 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.947 AC: 143875 AN: 151956 Hom.: 68176 Cov.: 31

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.947 AC: 143980 AN: 152074 Hom.: 68223 Cov.: 31 AF XY: 0.948 AC XY: 70511 AN XY: 74356

African (AFR) AF: 0.896 AC: 37135 AN: 41430

American (AMR) AF: 0.960 AC: 14670 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3282 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5170 AN: 5170

South Asian (SAS) AF: 0.983 AC: 4747 AN: 4830

European-Finnish (FIN) AF: 0.974 AC: 10332 AN: 10608

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65464 AN: 67960

Other (OTH) AF: 0.953 AC: 2014 AN: 2114

Alfa AF: 0.939 Hom.: 27454

Bravo AF: 0.942

Asia WGS AF: 0.984 AC: 3420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.17
DANN	Benign	0.47
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs7955401; hg19: chr12-52398751;