6-112372757-C-A

Variant names:

• chr6-112372757-C-A
• rs12717171

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 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

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;