rs3112740

Variant names:

• chr16-7786295-C-A
• rs3112740

Your query was ambiguous. Multiple possible variants found:

• chr16-7786295-C-A
• chr16-7786295-C-G
• chr16-7786295-C-T

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 0.13 in 150,640 control chromosomes in the GnomAD database, including 1,534 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 0.13 (1534 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 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: 0.130 AC: 19615 AN: 150532 Hom.: 1537 Cov.: 29

Gnomad AFR AF: 0.0870

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.130 AC: 19612 AN: 150640 Hom.: 1534 Cov.: 29 AF XY: 0.133 AC XY: 9774 AN XY: 73446

Gnomad4 AFR AF: 0.0870

Gnomad4 AMR AF: 0.0868

Gnomad4 ASJ AF: 0.0727

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.118

Alfa AF: 0.130 Hom.: 3255

Bravo AF: 0.118

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.5
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3112740; hg19: chr16-7836297;