5-3670892-C-A

Variant names:

• chr5-3670892-C-A
• rs1502644

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 0.855 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.633 AC: 26270 AN: 41502

American (AMR) AF: 0.929 AC: 14213 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3417 AN: 3472

East Asian (EAS) AF: 0.920 AC: 4764 AN: 5178

South Asian (SAS) AF: 0.984 AC: 4759 AN: 4834

European-Finnish (FIN) AF: 0.921 AC: 9774 AN: 10610

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63946 AN: 68032

Other (OTH) AF: 0.892 AC: 1883 AN: 2110

Alfa AF: 0.911 Hom.: 166658

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
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1502644; hg19: chr5-3671006;