6-131807424-C-T

Variant names:

• chr6-131807424-C-T
• rs1800949

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 0.179 in 152,160 control chromosomes in the GnomAD database, including 3,169 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 0.18 (3169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.246 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: 0.179 AC: 27240 AN: 152042 Hom.: 3166 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.179 AC: 27250 AN: 152160 Hom.: 3169 Cov.: 32 AF XY: 0.175 AC XY: 13038 AN XY: 74386

African (AFR) AF: 0.0450 AC: 1869 AN: 41538

American (AMR) AF: 0.253 AC: 3870 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3468

East Asian (EAS) AF: 0.182 AC: 938 AN: 5166

South Asian (SAS) AF: 0.147 AC: 710 AN: 4822

European-Finnish (FIN) AF: 0.164 AC: 1739 AN: 10594

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16777 AN: 67970

Other (OTH) AF: 0.171 AC: 361 AN: 2108

Alfa AF: 0.228 Hom.: 7168

Bravo AF: 0.185

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.7
DANN	Benign	0.80
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs1800949; hg19: chr6-132128564;