rs10511165

Variant names:

• chr3-98214539-A-G
• rs10511165

Your query was ambiguous. Multiple possible variants found:

• chr3-98214539-A-G
• chr3-98214539-A-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 0.099 in 152,164 control chromosomes in the GnomAD database, including 1,433 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 0.099 (1433 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.244 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: 0.0989 AC: 15036 AN: 152044 Hom.: 1433 Cov.: 33

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0426

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.0649

Gnomad NFE AF: 0.0352

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.0990 AC: 15059 AN: 152164 Hom.: 1433 Cov.: 33 AF XY: 0.0984 AC XY: 7321 AN XY: 74410

African (AFR) AF: 0.248 AC: 10301 AN: 41512

American (AMR) AF: 0.0425 AC: 649 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3470

East Asian (EAS) AF: 0.0894 AC: 464 AN: 5188

South Asian (SAS) AF: 0.102 AC: 491 AN: 4824

European-Finnish (FIN) AF: 0.0341 AC: 362 AN: 10602

Middle Eastern (MID) AF: 0.0621 AC: 18 AN: 290

European-Non Finnish (NFE) AF: 0.0352 AC: 2394 AN: 67976

Other (OTH) AF: 0.0868 AC: 183 AN: 2108

Alfa AF: 0.0895 Hom.: 166

Bravo AF: 0.105

Asia WGS AF: 0.0810 AC: 280 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.74
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10511165; hg19: chr3-97933383;