rs10515893

Variant names:

• chr5-165332490-G-A
• rs10515893

Your query was ambiguous. Multiple possible variants found:

• chr5-165332490-G-A
• chr5-165332490-G-C
• chr5-165332490-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 0.229 in 152,068 control chromosomes in the GnomAD database, including 4,257 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 0.23 (4257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 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: 0.229 AC: 34744 AN: 151950 Hom.: 4257 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.229 AC: 34748 AN: 152068 Hom.: 4257 Cov.: 32 AF XY: 0.228 AC XY: 16923 AN XY: 74358

African (AFR) AF: 0.148 AC: 6160 AN: 41496

American (AMR) AF: 0.210 AC: 3205 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3470

East Asian (EAS) AF: 0.157 AC: 812 AN: 5172

South Asian (SAS) AF: 0.303 AC: 1459 AN: 4822

European-Finnish (FIN) AF: 0.231 AC: 2442 AN: 10584

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18332 AN: 67932

Other (OTH) AF: 0.262 AC: 553 AN: 2110

Alfa AF: 0.259 Hom.: 22808

Bravo AF: 0.221

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10515893; hg19: chr5-164759496; COSMIC: COSV60227704;