rs10477360

Variant names:

• chr5-148024718-G-A
• rs10477360

Your query was ambiguous. Multiple possible variants found:

• chr5-148024718-G-A
• chr5-148024718-G-C
• chr5-148024718-G-T

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 0.437 in 151,870 control chromosomes in the GnomAD database, including 15,140 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 0.44 (15140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 9 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 (AMR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66305 AN: 151752 Hom.: 15138 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.437 AC: 66315 AN: 151870 Hom.: 15140 Cov.: 32 AF XY: 0.442 AC XY: 32833 AN XY: 74216

African (AFR) AF: 0.303 AC: 12561 AN: 41422

American (AMR) AF: 0.553 AC: 8429 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1558 AN: 3468

East Asian (EAS) AF: 0.494 AC: 2543 AN: 5148

South Asian (SAS) AF: 0.509 AC: 2448 AN: 4806

European-Finnish (FIN) AF: 0.512 AC: 5402 AN: 10556

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31744 AN: 67924

Other (OTH) AF: 0.467 AC: 986 AN: 2112

Alfa AF: 0.461 Hom.: 69969

Bravo AF: 0.438

Asia WGS AF: 0.520 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.68
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs10477360; hg19: chr5-147404281;