rs10503953

chr8-33940265-C-T

Variant summary

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

The ENST00000523063.5(ENSG00000253642):n.505-67591C>T variant causes a intron, non coding transcript 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: ENST00000523063.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379364	XR_002956701.2	n.288-67591C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523063.5	n.505-67591C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000523336.2	n.148-67591C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.364

Alfa AF: 0.408 Hom.: 6964

Bravo AF: 0.396

Asia WGS AF: 0.488 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.43
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503953; hg19: chr8-33797783;