rs7454108

Variant names:

• chr6-32713706-T-C
• rs7454108

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 0.0917 in 152,280 control chromosomes in the GnomAD database, including 816 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 0.092 (816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 103 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 (AMR) allele frequency at 95% confidence interval = 0.175 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: 0.0917 AC: 13950 AN: 152162 Hom.: 815 Cov.: 32

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0754

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0917 AC: 13970 AN: 152280 Hom.: 816 Cov.: 32 AF XY: 0.0936 AC XY: 6972 AN XY: 74462

African (AFR) AF: 0.0374 AC: 1554 AN: 41564

American (AMR) AF: 0.181 AC: 2763 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3468

East Asian (EAS) AF: 0.0758 AC: 393 AN: 5184

South Asian (SAS) AF: 0.0683 AC: 330 AN: 4830

European-Finnish (FIN) AF: 0.110 AC: 1163 AN: 10604

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6833 AN: 68020

Other (OTH) AF: 0.0904 AC: 191 AN: 2112

Alfa AF: 0.112 Hom.: 3510

Bravo AF: 0.0986

Asia WGS AF: 0.0600 AC: 211 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	7.4
DANN	Benign	0.49
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7454108; hg19: chr6-32681483;