rs7703402

Variant names:

• chr5-180360722-C-T
• rs7703402

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 0.103 in 152,174 control chromosomes in the GnomAD database, including 1,006 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 0.10 (1006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 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: 0.103 AC: 15637 AN: 152056 Hom.: 1005 Cov.: 32

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0996

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.103 AC: 15639 AN: 152174 Hom.: 1006 Cov.: 32 AF XY: 0.101 AC XY: 7492 AN XY: 74378

African (AFR) AF: 0.0402 AC: 1668 AN: 41534

American (AMR) AF: 0.0721 AC: 1103 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1112 AN: 5156

South Asian (SAS) AF: 0.0997 AC: 480 AN: 4816

European-Finnish (FIN) AF: 0.113 AC: 1191 AN: 10586

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9318 AN: 67998

Other (OTH) AF: 0.0995 AC: 210 AN: 2110

Alfa AF: 0.128 Hom.: 313

Bravo AF: 0.0949

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.81
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs7703402; hg19: chr5-179787722;