10-63943084-T-C

Position:

• chr10-63943084-T-C

Variant summary

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

The ENST00000654191.1(ENSG00000228566):​n.408-47185T>C 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 0.462 in 152,100 control chromosomes in the GnomAD database, including 17,835 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 0.46 (17835 hom., cov: 32)
• Consequence: ENST00000654191.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902439	XR_007062161.1	n.389-47185T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654191.1	n.408-47185T>C		intron_variant, non_coding_transcript_variant
	ENST00000444770.1	n.495-47185T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000660795.1	n.157-47185T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70233 AN: 151982 Hom.: 17824 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.462 AC: 70275 AN: 152100 Hom.: 17835 Cov.: 32 AF XY: 0.463 AC XY: 34464 AN XY: 74384

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.530

Alfa AF: 0.529 Hom.: 33712

Bravo AF: 0.464

Asia WGS AF: 0.537 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2252578; hg19: chr10-65702844;