rs10500410

Variant names:

• chr16-59034921-A-C
• rs10500410
• ENST00000500117.1:n.680-29261A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-59034921-A-C
• chr16-59034921-A-G
• chr16-59034921-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500117.1(ENSG00000245768):​n.680-29261A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,206 control chromosomes in the GnomAD database, including 2,060 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 (2060 hom., cov: 32)
• Consequence: ENSG00000245768 ENST00000500117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 0 publications found

Genes affected

ENSG00000245768 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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
ENSG00000245768	ENST00000500117.1	n.680-29261A>C		intron_variant	Intron 2 of 3	2
ENSG00000245768	ENST00000657379.1	n.651-29261A>C		intron_variant	Intron 2 of 3
ENSG00000245768	ENST00000730236.1	n.147+28594A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16864 AN: 152088 Hom.: 2056 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0277

Gnomad OTH AF: 0.0960

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

GnomAD4 genome AF: 0.111 AC: 16892 AN: 152206 Hom.: 2060 Cov.: 32 AF XY: 0.108 AC XY: 8016 AN XY: 74442

African (AFR) AF: 0.303 AC: 12547 AN: 41468

American (AMR) AF: 0.0569 AC: 871 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3472

East Asian (EAS) AF: 0.146 AC: 758 AN: 5184

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4826

European-Finnish (FIN) AF: 0.0134 AC: 142 AN: 10626

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0277 AC: 1886 AN: 68012

Other (OTH) AF: 0.0959 AC: 203 AN: 2116

Alfa AF: 0.0492 Hom.: 608

Bravo AF: 0.125

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.74
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10500410; hg19: chr16-59068825;