4-135961121-G-T

Variant names:

• chr4-135961121-G-T
• rs7679231

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 0.134 in 152,166 control chromosomes in the GnomAD database, including 2,426 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 0.13 (2426 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 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: 0.134 AC: 20342 AN: 152048 Hom.: 2416 Cov.: 33

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.134 AC: 20376 AN: 152166 Hom.: 2426 Cov.: 33 AF XY: 0.143 AC XY: 10636 AN XY: 74380

African (AFR) AF: 0.0491 AC: 2039 AN: 41538

American (AMR) AF: 0.260 AC: 3969 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3472

East Asian (EAS) AF: 0.611 AC: 3157 AN: 5168

South Asian (SAS) AF: 0.235 AC: 1132 AN: 4824

European-Finnish (FIN) AF: 0.166 AC: 1758 AN: 10582

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7408 AN: 68000

Other (OTH) AF: 0.138 AC: 291 AN: 2112

Alfa AF: 0.123 Hom.: 2968

Bravo AF: 0.141

Asia WGS AF: 0.408 AC: 1420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.39
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs7679231; hg19: chr4-136882276;