chr4-73751526-C-T

Variant names:

• chr4-73751526-C-T
• rs17202249

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 0.0694 in 151,960 control chromosomes in the GnomAD database, including 524 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 0.069 (524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0998 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: 0.0695 AC: 10558 AN: 151842 Hom.: 524 Cov.: 32

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0425

Gnomad FIN AF: 0.0377

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0694 AC: 10548 AN: 151960 Hom.: 524 Cov.: 32 AF XY: 0.0663 AC XY: 4927 AN XY: 74266

African (AFR) AF: 0.0173 AC: 718 AN: 41494

American (AMR) AF: 0.0976 AC: 1486 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5148

South Asian (SAS) AF: 0.0421 AC: 203 AN: 4824

European-Finnish (FIN) AF: 0.0377 AC: 400 AN: 10600

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6916 AN: 67902

Other (OTH) AF: 0.0998 AC: 210 AN: 2104

Alfa AF: 0.0788 Hom.: 405

Bravo AF: 0.0723

Asia WGS AF: 0.0190 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.76
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17202249; hg19: chr4-74617243;