10-63917874-C-T

Position:

• chr10-63917874-C-T

Variant summary

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

The ENST00000654191.1(ENSG00000228566):​n.407+44898C>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 0.6 in 151,932 control chromosomes in the GnomAD database, including 27,673 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 0.60 (27673 hom., cov: 31)
• Consequence: ENST00000654191.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902439	XR_007062161.1	n.388+44898C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654191.1	n.407+44898C>T		intron_variant, non_coding_transcript_variant
	ENST00000444770.1	n.495-72395C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000660795.1	n.156+30786C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91126 AN: 151814 Hom.: 27645 Cov.: 31

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.600 AC: 91201 AN: 151932 Hom.: 27673 Cov.: 31 AF XY: 0.603 AC XY: 44773 AN XY: 74240

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.643

Alfa AF: 0.631 Hom.: 40844

Bravo AF: 0.602

Asia WGS AF: 0.584 AC: 2029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.8
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2244205; hg19: chr10-65677634;