rs10503985

Variant names:

• chr8-36156306-G-A
• rs10503985
• ENST00000659919.1:n.175+9620G>A

Variant summary

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

The ENST00000659919.1(ENSG00000253452):​n.175+9620G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 152,292 control chromosomes in the GnomAD database, including 62 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 0.021 (62 hom., cov: 32)
• Consequence: ENSG00000253452 ENST00000659919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

Genes affected

ENSG00000253452 (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 (EAS) allele frequency at 95% confidence interval = 0.109 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
ENSG00000253452	ENST00000659919.1	n.175+9620G>A		intron_variant	Intron 3 of 7
ENSG00000253452	ENST00000662333.1	n.224-20279G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0209 AC: 3180 AN: 152174 Hom.: 62 Cov.: 32

Gnomad AFR AF: 0.0238

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00871

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0631

Gnomad FIN AF: 0.0387

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00988

Gnomad OTH AF: 0.0205

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

GnomAD4 genome AF: 0.0209 AC: 3189 AN: 152292 Hom.: 62 Cov.: 32 AF XY: 0.0234 AC XY: 1743 AN XY: 74464

Gnomad4 AFR AF: 0.0238

Gnomad4 AMR AF: 0.00870

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.0636

Gnomad4 FIN AF: 0.0387

Gnomad4 NFE AF: 0.00989

Gnomad4 OTH AF: 0.0222

Alfa AF: 0.0170 Hom.: 7

Bravo AF: 0.0188

Asia WGS AF: 0.0970 AC: 337 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	3.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503985; hg19: chr8-36013824;