rs12717171

chr6-112372757-C-Achr6-112372757-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 0.372 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.335

Alfa AF: 0.443 Hom.: 14378

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

Splicing

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

Publications

LitVar

Other links and lift over

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