chr4-126395828-G-A

Variant names:

• chr4-126395828-G-A
• rs7683488

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 0.151 in 151,886 control chromosomes in the GnomAD database, including 1,949 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 (1949 hom., cov: 31)
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 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: 0.151 AC: 22916 AN: 151768 Hom.: 1947 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0251

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.151 AC: 22937 AN: 151886 Hom.: 1949 Cov.: 31 AF XY: 0.151 AC XY: 11233 AN XY: 74206

African (AFR) AF: 0.203 AC: 8404 AN: 41420

American (AMR) AF: 0.104 AC: 1581 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3468

East Asian (EAS) AF: 0.0250 AC: 128 AN: 5118

South Asian (SAS) AF: 0.233 AC: 1124 AN: 4818

European-Finnish (FIN) AF: 0.143 AC: 1512 AN: 10566

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9254 AN: 67960

Other (OTH) AF: 0.142 AC: 298 AN: 2096

Alfa AF: 0.157 Hom.: 288

Bravo AF: 0.145

Asia WGS AF: 0.130 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.70
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs7683488; hg19: chr4-127316983;