5-126866468-T-G

Variant names:

• chr5-126866468-T-G
• rs7738021

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 0.758 in 152,016 control chromosomes in the GnomAD database, including 44,837 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 0.76 (44837 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 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: 0.758 AC: 115110 AN: 151898 Hom.: 44770 Cov.: 30

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.758 AC: 115241 AN: 152016 Hom.: 44837 Cov.: 30 AF XY: 0.751 AC XY: 55747 AN XY: 74272

African (AFR) AF: 0.944 AC: 39230 AN: 41544

American (AMR) AF: 0.765 AC: 11676 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2425 AN: 3470

East Asian (EAS) AF: 0.729 AC: 3765 AN: 5162

South Asian (SAS) AF: 0.603 AC: 2888 AN: 4792

European-Finnish (FIN) AF: 0.590 AC: 6217 AN: 10530

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46564 AN: 67952

Other (OTH) AF: 0.756 AC: 1590 AN: 2104

Alfa AF: 0.715 Hom.: 84671

Bravo AF: 0.783

Asia WGS AF: 0.671 AC: 2335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.80
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7738021; hg19: chr5-126202160;