6-110424403-G-T

Variant names:

• chr6-110424403-G-T
• rs6938431

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 0.216 in 114,484 control chromosomes in the GnomAD database, including 2,169 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 0.22 (2169 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.374 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: 0.216 AC: 24748 AN: 114452 Hom.: 2161 Cov.: 30

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.216 AC: 24771 AN: 114484 Hom.: 2169 Cov.: 30 AF XY: 0.213 AC XY: 11801 AN XY: 55312

African (AFR) AF: 0.380 AC: 8690 AN: 22844

American (AMR) AF: 0.115 AC: 1446 AN: 12616

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 497 AN: 3152

East Asian (EAS) AF: 0.140 AC: 330 AN: 2364

South Asian (SAS) AF: 0.194 AC: 644 AN: 3312

European-Finnish (FIN) AF: 0.171 AC: 1354 AN: 7912

Middle Eastern (MID) AF: 0.203 AC: 50 AN: 246

European-Non Finnish (NFE) AF: 0.188 AC: 11183 AN: 59498

Other (OTH) AF: 0.193 AC: 327 AN: 1696

Alfa AF: 0.163 Hom.: 3701

Bravo AF: 0.162

Asia WGS AF: 0.160 AC: 433 AN: 2712

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6938431; hg19: chr6-110745606;