rs7955516

Variant names:

• chr12-20345102-A-C
• rs7955516

Your query was ambiguous. Multiple possible variants found:

• chr12-20345102-A-C
• chr12-20345102-A-G
• chr12-20345102-A-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 0.357 in 145,616 control chromosomes in the GnomAD database, including 9,261 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 (9261 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 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: 0.357 AC: 51988 AN: 145494 Hom.: 9253 Cov.: 29

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.451

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.357 AC: 52024 AN: 145616 Hom.: 9261 Cov.: 29 AF XY: 0.352 AC XY: 25055 AN XY: 71198

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.383

Alfa AF: 0.356 Hom.: 8125

Bravo AF: 0.351

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.016
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7955516; hg19: chr12-20498036;