rs12717171

Variant names:

• chr6-112372757-C-A
• rs12717171

Your query was ambiguous. Multiple possible variants found:

• chr6-112372757-C-A
• chr6-112372757-C-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 0.372 in 152,068 control chromosomes in the GnomAD database, including 12,830 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 0.37 (12830 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 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: 0.373 AC: 56616 AN: 151950 Hom.: 12833 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.372 AC: 56622 AN: 152068 Hom.: 12830 Cov.: 33 AF XY: 0.377 AC XY: 28006 AN XY: 74310

African (AFR) AF: 0.128 AC: 5327 AN: 41492

American (AMR) AF: 0.285 AC: 4355 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1195 AN: 3466

East Asian (EAS) AF: 0.409 AC: 2114 AN: 5168

South Asian (SAS) AF: 0.432 AC: 2083 AN: 4826

European-Finnish (FIN) AF: 0.646 AC: 6832 AN: 10576

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33429 AN: 67950

Other (OTH) AF: 0.335 AC: 708 AN: 2112

Alfa AF: 0.425 Hom.: 18127

Bravo AF: 0.332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.80
DANN	Benign	0.71
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs12717171; hg19: chr6-112693959; COSMIC: COSV60266570;