chr6-43762018-G-T

Variant names:

• chr6-43762018-G-T
• rs1109324

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 0.145 in 152,210 control chromosomes in the GnomAD database, including 1,591 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 0.15 (1591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 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: 0.145 AC: 22097 AN: 152092 Hom.: 1589 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.145 AC: 22116 AN: 152210 Hom.: 1591 Cov.: 32 AF XY: 0.148 AC XY: 10982 AN XY: 74432

African (AFR) AF: 0.134 AC: 5559 AN: 41520

American (AMR) AF: 0.138 AC: 2109 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3472

East Asian (EAS) AF: 0.102 AC: 529 AN: 5178

South Asian (SAS) AF: 0.141 AC: 679 AN: 4828

European-Finnish (FIN) AF: 0.166 AC: 1760 AN: 10598

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10523 AN: 68000

Other (OTH) AF: 0.124 AC: 263 AN: 2114

Alfa AF: 0.125 Hom.: 570

Bravo AF: 0.138

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.56
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs1109324; hg19: chr6-43729755;