6-81418669-T-C

Variant names:

• chr6-81418669-T-C
• rs17529111

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 0.18 in 152,036 control chromosomes in the GnomAD database, including 2,912 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 (2912 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.235 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: 0.180 AC: 27295 AN: 151918 Hom.: 2911 Cov.: 32

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.180 AC: 27297 AN: 152036 Hom.: 2912 Cov.: 32 AF XY: 0.183 AC XY: 13605 AN XY: 74316

African (AFR) AF: 0.0673 AC: 2797 AN: 41558

American (AMR) AF: 0.241 AC: 3677 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 858 AN: 3468

East Asian (EAS) AF: 0.200 AC: 1032 AN: 5160

South Asian (SAS) AF: 0.206 AC: 991 AN: 4822

European-Finnish (FIN) AF: 0.282 AC: 2984 AN: 10566

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14279 AN: 67906

Other (OTH) AF: 0.201 AC: 424 AN: 2112

Alfa AF: 0.204 Hom.: 4677

Bravo AF: 0.172

Asia WGS AF: 0.187 AC: 648 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	2.2
DANN	Benign	0.46
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs17529111; hg19: chr6-82128386;