rs10503953

Variant names:

• chr8-33940265-C-T
• rs10503953
• ENST00000521541.2:n.314-67591C>T

Variant summary

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

The ENST00000521541.2(ENSG00000253642):​n.314-67591C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,928 control chromosomes in the GnomAD database, including 12,492 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 0.40 (12492 hom., cov: 32)
• Consequence: ENSG00000253642 ENST00000521541.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 1 publications found

Genes affected

ENSG00000253642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521541.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105379364	NR_189605.1		n.746-94621C>T		intron	N/A
	LOC105379364	NR_189606.1		n.331-67591C>T		intron	N/A
	LOC105379364	NR_189607.1		n.330+143829C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253642	ENST00000521541.2	TSL:2	n.314-67591C>T		intron	N/A
	ENSG00000253642	ENST00000523063.5	TSL:3	n.505-67591C>T		intron	N/A
	ENSG00000253642	ENST00000523336.2	TSL:2	n.148-67591C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61197 AN: 151810 Hom.: 12484 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.403 AC: 61229 AN: 151928 Hom.: 12492 Cov.: 32 AF XY: 0.402 AC XY: 29879 AN XY: 74260

African (AFR) AF: 0.386 AC: 15982 AN: 41422

American (AMR) AF: 0.367 AC: 5603 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3470

East Asian (EAS) AF: 0.496 AC: 2549 AN: 5136

South Asian (SAS) AF: 0.507 AC: 2444 AN: 4818

European-Finnish (FIN) AF: 0.409 AC: 4312 AN: 10548

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28069 AN: 67954

Other (OTH) AF: 0.364 AC: 768 AN: 2108

Alfa AF: 0.407 Hom.: 9381

Bravo AF: 0.396

Asia WGS AF: 0.488 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.35
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10503953; hg19: chr8-33797783;