rs1246182

Variant names:

• chr6-156648182-G-A
• rs1246182

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 0.575 in 152,012 control chromosomes in the GnomAD database, including 25,222 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 0.57 (25222 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.73 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: 0.574 AC: 87251 AN: 151894 Hom.: 25186 Cov.: 31

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.575 AC: 87340 AN: 152012 Hom.: 25222 Cov.: 31 AF XY: 0.578 AC XY: 42938 AN XY: 74276

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.575

Alfa AF: 0.581 Hom.: 20834

Bravo AF: 0.582

Asia WGS AF: 0.653 AC: 2268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.020
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1246182; hg19: chr6-156969316; COSMIC: COSV69431341;