chr4-72649596-T-C

Variant names:

• chr4-72649596-T-C
• rs7697556

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.431 in 152,128 control chromosomes in the GnomAD database, including 15,798 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 0.43 (15798 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.39
• Publications: 46 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 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: 0.431 AC: 65488 AN: 152010 Hom.: 15789 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.431 AC: 65517 AN: 152128 Hom.: 15798 Cov.: 33 AF XY: 0.434 AC XY: 32264 AN XY: 74358

African (AFR) AF: 0.201 AC: 8339 AN: 41536

American (AMR) AF: 0.568 AC: 8673 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2081 AN: 3470

East Asian (EAS) AF: 0.463 AC: 2385 AN: 5148

South Asian (SAS) AF: 0.362 AC: 1744 AN: 4820

European-Finnish (FIN) AF: 0.513 AC: 5431 AN: 10578

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.517 AC: 35135 AN: 67990

Other (OTH) AF: 0.474 AC: 1000 AN: 2110

Alfa AF: 0.494 Hom.: 56248

Bravo AF: 0.435

Asia WGS AF: 0.353 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	20
DANN	Benign	0.79
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs7697556; hg19: chr4-73515313;