rs10763625

Positions:

• chr10-18746022-C-T

Variant summary

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

The ENST00000654305.1(ENSG00000234244):​n.94-667C>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 0.17 in 152,132 control chromosomes in the GnomAD database, including 2,369 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 0.17 (2369 hom., cov: 32)
• Consequence: ENST00000654305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376440	XR_930721.2	n.69-667C>T		intron_variant, non_coding_transcript_variant
LOC105376440	XR_930720.2	n.52-32270C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654305.1	n.94-667C>T		intron_variant, non_coding_transcript_variant
	ENST00000654415.1	n.220+623C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25829 AN: 152014 Hom.: 2367 Cov.: 32

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.170 AC: 25840 AN: 152132 Hom.: 2369 Cov.: 32 AF XY: 0.169 AC XY: 12571 AN XY: 74372

Gnomad4 AFR AF: 0.0967

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.164

Alfa AF: 0.197 Hom.: 3889

Bravo AF: 0.164

Asia WGS AF: 0.179 AC: 620 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10763625; hg19: chr10-19034951;