rs4731402

Variant names:

• chr7-128143884-T-C
• rs4731402

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 0.163 in 152,098 control chromosomes in the GnomAD database, including 2,246 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 0.16 (2246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 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: 0.163 AC: 24725 AN: 151978 Hom.: 2240 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.163 AC: 24755 AN: 152098 Hom.: 2246 Cov.: 32 AF XY: 0.163 AC XY: 12111 AN XY: 74372

African (AFR) AF: 0.233 AC: 9675 AN: 41466

American (AMR) AF: 0.158 AC: 2424 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 489 AN: 3472

East Asian (EAS) AF: 0.193 AC: 997 AN: 5166

South Asian (SAS) AF: 0.235 AC: 1134 AN: 4818

European-Finnish (FIN) AF: 0.104 AC: 1098 AN: 10580

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8459 AN: 67988

Other (OTH) AF: 0.170 AC: 359 AN: 2110

Alfa AF: 0.147 Hom.: 295

Bravo AF: 0.169

Asia WGS AF: 0.246 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.5
DANN	Benign	0.27
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs4731402; hg19: chr7-127783936;