rs7702361

chr5-33935838-A-Cchr5-33935838-A-Gchr5-33935838-A-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 0.662 in 152,090 control chromosomes in the GnomAD database, including 35,091 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 0.66 (35091 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100549 AN: 151972 Hom.: 35027 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.662 AC: 100670 AN: 152090 Hom.: 35091 Cov.: 32 AF XY: 0.666 AC XY: 49480 AN XY: 74322

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.670

Alfa AF: 0.567 Hom.: 14166

Bravo AF: 0.681

Asia WGS AF: 0.802 AC: 2787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.2
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7702361; hg19: chr5-33935943;