6-20395026-C-T

Variant names:

• chr6-20395026-C-T
• rs6915426

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 0.157 in 151,966 control chromosomes in the GnomAD database, including 2,042 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 0.16 (2042 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 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: 0.157 AC: 23867 AN: 151848 Hom.: 2028 Cov.: 31

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.00673

Gnomad SAS AF: 0.0772

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.157 AC: 23909 AN: 151966 Hom.: 2042 Cov.: 31 AF XY: 0.154 AC XY: 11437 AN XY: 74260

African (AFR) AF: 0.199 AC: 8232 AN: 41420

American (AMR) AF: 0.122 AC: 1866 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 427 AN: 3470

East Asian (EAS) AF: 0.00675 AC: 35 AN: 5186

South Asian (SAS) AF: 0.0771 AC: 372 AN: 4826

European-Finnish (FIN) AF: 0.139 AC: 1463 AN: 10522

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10895 AN: 67952

Other (OTH) AF: 0.158 AC: 333 AN: 2106

Alfa AF: 0.153 Hom.: 3163

Bravo AF: 0.158

Asia WGS AF: 0.0610 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.51
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs6915426; hg19: chr6-20395257;