7-152889438-T-C

Variant names:

• chr7-152889438-T-C
• rs4726220

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 0.801 in 152,218 control chromosomes in the GnomAD database, including 51,700 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 0.80 (51700 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.926 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: 0.802 AC: 121946 AN: 152100 Hom.: 51683 Cov.: 33

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.801 AC: 121997 AN: 152218 Hom.: 51700 Cov.: 33 AF XY: 0.804 AC XY: 59877 AN XY: 74442

African (AFR) AF: 0.496 AC: 20550 AN: 41472

American (AMR) AF: 0.896 AC: 13705 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3021 AN: 3472

East Asian (EAS) AF: 0.888 AC: 4597 AN: 5178

South Asian (SAS) AF: 0.795 AC: 3840 AN: 4832

European-Finnish (FIN) AF: 0.947 AC: 10059 AN: 10620

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.932 AC: 63419 AN: 68026

Other (OTH) AF: 0.818 AC: 1727 AN: 2112

Alfa AF: 0.886 Hom.: 13103

Bravo AF: 0.788

Asia WGS AF: 0.816 AC: 2841 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	2.3
DANN	Benign	0.38
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs4726220; hg19: chr7-152586523;