rs10510310

Variant names:

• chr3-5470948-A-C
• rs10510310

Your query was ambiguous. Multiple possible variants found:

• chr3-5470948-A-C
• chr3-5470948-A-G

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 0.112 in 152,094 control chromosomes in the GnomAD database, including 1,029 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 0.11 (1029 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.142 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: 0.112 AC: 17040 AN: 151976 Hom.: 1015 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.0893

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.0896

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

GnomAD4 genome AF: 0.112 AC: 17095 AN: 152094 Hom.: 1029 Cov.: 32 AF XY: 0.114 AC XY: 8505 AN XY: 74378

African (AFR) AF: 0.141 AC: 5839 AN: 41518

American (AMR) AF: 0.120 AC: 1839 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3468

East Asian (EAS) AF: 0.0893 AC: 462 AN: 5172

South Asian (SAS) AF: 0.151 AC: 726 AN: 4810

European-Finnish (FIN) AF: 0.0998 AC: 1060 AN: 10616

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0975 AC: 6622 AN: 67930

Other (OTH) AF: 0.0967 AC: 204 AN: 2110

Alfa AF: 0.105 Hom.: 1093

Bravo AF: 0.114

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.73
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs10510310; hg19: chr3-5512635;