rs10491480

Variant names:

• chr5-39478674-T-C
• rs10491480

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 0.0473 in 151,546 control chromosomes in the GnomAD database, including 192 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 0.047 (192 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.890
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0673 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: 0.0473 AC: 7163 AN: 151434 Hom.: 192 Cov.: 31

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0406

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0492

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0432

Gnomad OTH AF: 0.0422

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

GnomAD4 genome AF: 0.0473 AC: 7169 AN: 151546 Hom.: 192 Cov.: 31 AF XY: 0.0461 AC XY: 3416 AN XY: 74076

African (AFR) AF: 0.0694 AC: 2876 AN: 41434

American (AMR) AF: 0.0405 AC: 616 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3466

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5182

South Asian (SAS) AF: 0.0499 AC: 240 AN: 4812

European-Finnish (FIN) AF: 0.0277 AC: 286 AN: 10308

Middle Eastern (MID) AF: 0.0172 AC: 5 AN: 290

European-Non Finnish (NFE) AF: 0.0433 AC: 2935 AN: 67846

Other (OTH) AF: 0.0418 AC: 88 AN: 2106

Alfa AF: 0.0471 Hom.: 45

Bravo AF: 0.0482

Asia WGS AF: 0.0220 AC: 76 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.62
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs10491480; hg19: chr5-39478776;