10-62498069-T-C

Variant names:

• chr10-62498069-T-C
• rs10509168
• ENST00000647733.1:c.981+38272T>C

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.981+38272T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,080 control chromosomes in the GnomAD database, including 15,462 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 0.43 (15462 hom., cov: 32)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.698

Genes affected

ENSG00000285837 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 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
ENSG00000285837	ENST00000647733.1	c.981+38272T>C		intron_variant	Intron 4 of 7			ENSP00000502188.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65241 AN: 151962 Hom.: 15467 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.429 AC: 65240 AN: 152080 Hom.: 15462 Cov.: 32 AF XY: 0.432 AC XY: 32102 AN XY: 74334

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.464

Alfa AF: 0.514 Hom.: 29144

Bravo AF: 0.421

Asia WGS AF: 0.455 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	5.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509168; hg19: chr10-64257828;