rs10515002

Variant names:

• chr5-66327805-G-A
• rs10515002
• ENST00000663200.1:n.371+9379G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-66327805-G-A
• chr5-66327805-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663200.1(ENSG00000251391):​n.371+9379G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,182 control chromosomes in the GnomAD database, including 2,357 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 0.10 (2357 hom., cov: 32)
• Consequence: ENSG00000251391 ENST00000663200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

Genes affected

ENSG00000251391 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 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
ENSG00000251391	ENST00000663200.1	n.371+9379G>A		intron_variant	Intron 3 of 4
ENSG00000251391	ENST00000665668.1	n.394+4865G>A		intron_variant	Intron 3 of 4
ENSG00000251391	ENST00000666197.1	n.382+4823G>A		intron_variant	Intron 3 of 3
ENSG00000251391	ENST00000668388.1	n.393-1015G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15418 AN: 152064 Hom.: 2348 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.00763

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00561

Gnomad OTH AF: 0.0749

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

GnomAD4 genome AF: 0.102 AC: 15466 AN: 152182 Hom.: 2357 Cov.: 32 AF XY: 0.0978 AC XY: 7275 AN XY: 74408

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.0530

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0226

Gnomad4 FIN AF: 0.00763

Gnomad4 NFE AF: 0.00562

Gnomad4 OTH AF: 0.0741

Alfa AF: 0.0547 Hom.: 340

Bravo AF: 0.116

Asia WGS AF: 0.0490 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515002; hg19: chr5-65623633;