4-99364194-G-A

Variant names:

• chr4-99364194-G-A
• rs1154436

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 0.232 in 151,982 control chromosomes in the GnomAD database, including 4,836 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 0.23 (4836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 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: 0.232 AC: 35247 AN: 151864 Hom.: 4833 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0217

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.232 AC: 35260 AN: 151982 Hom.: 4836 Cov.: 32 AF XY: 0.231 AC XY: 17138 AN XY: 74294

African (AFR) AF: 0.117 AC: 4831 AN: 41464

American (AMR) AF: 0.199 AC: 3035 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3470

East Asian (EAS) AF: 0.0218 AC: 113 AN: 5188

South Asian (SAS) AF: 0.206 AC: 989 AN: 4808

European-Finnish (FIN) AF: 0.370 AC: 3902 AN: 10546

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20888 AN: 67926

Other (OTH) AF: 0.212 AC: 445 AN: 2104

Alfa AF: 0.256 Hom.: 1998

Bravo AF: 0.212

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.76
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1154436; hg19: chr4-100285351;