rs7964407

Variant names:

• chr12-28040056-G-A
• rs7964407

Your query was ambiguous. Multiple possible variants found:

• chr12-28040056-G-A
• chr12-28040056-G-T

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 0.353 in 152,038 control chromosomes in the GnomAD database, including 10,055 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 (10055 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 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: 0.353 AC: 53687 AN: 151920 Hom.: 10040 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.353 AC: 53740 AN: 152038 Hom.: 10055 Cov.: 32 AF XY: 0.348 AC XY: 25859 AN XY: 74338

African (AFR) AF: 0.473 AC: 19618 AN: 41436

American (AMR) AF: 0.271 AC: 4145 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1319 AN: 5174

South Asian (SAS) AF: 0.252 AC: 1214 AN: 4812

European-Finnish (FIN) AF: 0.320 AC: 3375 AN: 10556

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.323 AC: 21993 AN: 67986

Other (OTH) AF: 0.318 AC: 671 AN: 2112

Alfa AF: 0.334 Hom.: 24904

Bravo AF: 0.358

Asia WGS AF: 0.259 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.66
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs7964407; hg19: chr12-28192989;