rs7965445

Variant names:

• chr12-131378358-G-A
• rs7965445

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 0.169 in 150,066 control chromosomes in the GnomAD database, including 3,456 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 0.17 (3456 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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: 0.169 AC: 25333 AN: 149942 Hom.: 3450 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.00776

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.00120

Gnomad SAS AF: 0.0693

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.169 AC: 25379 AN: 150066 Hom.: 3456 Cov.: 31 AF XY: 0.165 AC XY: 12085 AN XY: 73380

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.0938

Gnomad4 ASJ AF: 0.0801

Gnomad4 EAS AF: 0.00120

Gnomad4 SAS AF: 0.0704

Gnomad4 FIN AF: 0.0985

Gnomad4 NFE AF: 0.0911

Gnomad4 OTH AF: 0.152

Alfa AF: 0.0933 Hom.: 882

Bravo AF: 0.177

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.3
CADD	Benign	1.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7965445; hg19: chr12-131862903;