rs1502644

Positions:

• chr5-3670892-C-A
• chr5-3670892-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 0.855 in 152,244 control chromosomes in the GnomAD database, including 57,139 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 0.86 (57139 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.961 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: 0.855 AC: 130106 AN: 152126 Hom.: 57115 Cov.: 34

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.985

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.855 AC: 130187 AN: 152244 Hom.: 57139 Cov.: 34 AF XY: 0.860 AC XY: 64009 AN XY: 74442

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.929

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.984

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.940

Gnomad4 OTH AF: 0.892

Alfa AF: 0.935 Hom.: 121688

Bravo AF: 0.845

Asia WGS AF: 0.938 AC: 3260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.35
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1502644; hg19: chr5-3671006;