rs7310342

Variant names:

• chr12-43222842-G-A
• rs7310342

Your query was ambiguous. Multiple possible variants found:

• chr12-43222842-G-A
• chr12-43222842-G-C

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 0.36 in 152,030 control chromosomes in the GnomAD database, including 10,486 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 0.36 (10486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 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: 0.360 AC: 54654 AN: 151912 Hom.: 10471 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.360 AC: 54703 AN: 152030 Hom.: 10486 Cov.: 32 AF XY: 0.369 AC XY: 27429 AN XY: 74304

African (AFR) AF: 0.247 AC: 10220 AN: 41458

American (AMR) AF: 0.467 AC: 7139 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1490 AN: 3470

East Asian (EAS) AF: 0.467 AC: 2411 AN: 5164

South Asian (SAS) AF: 0.550 AC: 2652 AN: 4818

European-Finnish (FIN) AF: 0.395 AC: 4172 AN: 10560

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25298 AN: 67964

Other (OTH) AF: 0.385 AC: 812 AN: 2110

Alfa AF: 0.377 Hom.: 49865

Bravo AF: 0.363

Asia WGS AF: 0.468 AC: 1628 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.44
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs7310342; hg19: chr12-43616645;