6-18791492-C-T

Variant names:

• chr6-18791492-C-T
• rs41441749

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 0.19 in 152,000 control chromosomes in the GnomAD database, including 2,846 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 0.19 (2846 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 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: 0.190 AC: 28855 AN: 151882 Hom.: 2848 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.190 AC: 28855 AN: 152000 Hom.: 2846 Cov.: 32 AF XY: 0.190 AC XY: 14146 AN XY: 74286

African (AFR) AF: 0.194 AC: 8038 AN: 41470

American (AMR) AF: 0.215 AC: 3285 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3464

East Asian (EAS) AF: 0.110 AC: 567 AN: 5152

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4820

European-Finnish (FIN) AF: 0.193 AC: 2041 AN: 10568

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12438 AN: 67962

Other (OTH) AF: 0.202 AC: 426 AN: 2112

Alfa AF: 0.179 Hom.: 7383

Bravo AF: 0.193

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.69
DANN	Benign	0.78
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs41441749; hg19: chr6-18791723; COSMIC: COSV71233049;