chr10-88106892-C-T

Variant names:

• chr10-88106892-C-T
• rs11202656
• ENST00000752267.1:n.649-25361C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000752267.1(ENSG00000297977):​n.649-25361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,086 control chromosomes in the GnomAD database, including 5,117 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 0.25 (5117 hom., cov: 33)
• Consequence: ENSG00000297977 ENST00000752267.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 4 publications found

Genes affected

ENSG00000297977 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752267.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297977	ENST00000752267.1		n.649-25361C>T		intron	N/A
	ENSG00000297977	ENST00000752268.1		n.675-25361C>T		intron	N/A
	ENSG00000297977	ENST00000752271.1		n.263-25535C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37945 AN: 151968 Hom.: 5119 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.249 AC: 37943 AN: 152086 Hom.: 5117 Cov.: 33 AF XY: 0.252 AC XY: 18735 AN XY: 74336

African (AFR) AF: 0.179 AC: 7419 AN: 41464

American (AMR) AF: 0.197 AC: 3008 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 876 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2420 AN: 5164

South Asian (SAS) AF: 0.319 AC: 1536 AN: 4818

European-Finnish (FIN) AF: 0.279 AC: 2953 AN: 10572

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18938 AN: 67996

Other (OTH) AF: 0.243 AC: 513 AN: 2108

Alfa AF: 0.265 Hom.: 17326

Bravo AF: 0.239

Asia WGS AF: 0.349 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.66
DANN	Benign	0.42
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11202656; hg19: chr10-89866649;