rs10500409

Variant names:

• chr16-58966183-A-G
• rs10500409
• ENST00000500117.1:n.680-97999A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-58966183-A-G
• chr16-58966183-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.680-97999A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 152,262 control chromosomes in the GnomAD database, including 316 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 0.042 (316 hom., cov: 33)
• Consequence: ENSG00000245768 ENST00000500117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362
• 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 (EAS) allele frequency at 95% confidence interval = 0.11 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.680-97999A>G		intron_variant	Intron 2 of 3	2
ENSG00000245768	ENST00000657379.1	n.651-97999A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0420 AC: 6395 AN: 152144 Hom.: 314 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0308

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00791

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0421 AC: 6413 AN: 152262 Hom.: 316 Cov.: 33 AF XY: 0.0405 AC XY: 3017 AN XY: 74448

African (AFR) AF: 0.111 AC: 4610 AN: 41528

American (AMR) AF: 0.0233 AC: 357 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3472

East Asian (EAS) AF: 0.118 AC: 612 AN: 5180

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4828

European-Finnish (FIN) AF: 0.00141 AC: 15 AN: 10622

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00791 AC: 538 AN: 68024

Other (OTH) AF: 0.0436 AC: 92 AN: 2110

Alfa AF: 0.0292 Hom.: 23

Bravo AF: 0.0471

Asia WGS AF: 0.0720 AC: 252 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	3.6
DANN	Benign	0.52
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10500409; hg19: chr16-59000087;