rs4075154

Variant names:

• chr8-56296687-A-G
• rs4075154

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 0.195 in 152,138 control chromosomes in the GnomAD database, including 3,656 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 0.20 (3656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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: 0.195 AC: 29616 AN: 152020 Hom.: 3638 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0563

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.195 AC: 29675 AN: 152138 Hom.: 3656 Cov.: 32 AF XY: 0.192 AC XY: 14306 AN XY: 74400

African (AFR) AF: 0.355 AC: 14720 AN: 41464

American (AMR) AF: 0.171 AC: 2608 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3472

East Asian (EAS) AF: 0.0560 AC: 290 AN: 5176

South Asian (SAS) AF: 0.122 AC: 591 AN: 4828

European-Finnish (FIN) AF: 0.130 AC: 1381 AN: 10610

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8861 AN: 67984

Other (OTH) AF: 0.199 AC: 419 AN: 2106

Alfa AF: 0.161 Hom.: 4752

Bravo AF: 0.206

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.85
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs4075154; hg19: chr8-57209246;