rs4731530

Variant names:

• chr7-128922524-T-C
• rs4731530

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 0.529 in 152,074 control chromosomes in the GnomAD database, including 21,441 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 0.53 (21441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 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: 0.529 AC: 80379 AN: 151954 Hom.: 21426 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.529 AC: 80432 AN: 152074 Hom.: 21441 Cov.: 32 AF XY: 0.528 AC XY: 39225 AN XY: 74346

African (AFR) AF: 0.537 AC: 22281 AN: 41462

American (AMR) AF: 0.508 AC: 7760 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2186 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2195 AN: 5174

South Asian (SAS) AF: 0.550 AC: 2650 AN: 4818

European-Finnish (FIN) AF: 0.534 AC: 5639 AN: 10566

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35839 AN: 67990

Other (OTH) AF: 0.548 AC: 1152 AN: 2104

Alfa AF: 0.527 Hom.: 38716

Bravo AF: 0.527

Asia WGS AF: 0.497 AC: 1730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.55
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4731530; hg19: chr7-128562578;