rs7703402

Positions:

• chr5-180360722-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0402

Gnomad4 AMR AF: 0.0721

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.0997

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.0995

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7703402; hg19: chr5-179787722;