chr10-52778780-C-T

Variant names:

• chr10-52778780-C-T
• rs11003136
• ENST00000816985.1:n.135-139G>A

Variant summary

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

The ENST00000816985.1(ENSG00000306325):​n.135-139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,046 control chromosomes in the GnomAD database, including 10,104 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 0.36 (10104 hom., cov: 32)
• Consequence: ENSG00000306325 ENST00000816985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 9 publications found

Genes affected

ENSG00000306325 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816985.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306325	ENST00000816985.1		n.135-139G>A		intron	N/A
	ENSG00000306279	ENST00000816735.1		n.-175C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54922 AN: 151928 Hom.: 10098 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.361 AC: 54946 AN: 152046 Hom.: 10104 Cov.: 32 AF XY: 0.361 AC XY: 26827 AN XY: 74304

African (AFR) AF: 0.323 AC: 13398 AN: 41466

American (AMR) AF: 0.375 AC: 5737 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1641 AN: 5134

South Asian (SAS) AF: 0.417 AC: 2007 AN: 4808

European-Finnish (FIN) AF: 0.341 AC: 3614 AN: 10590

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.378 AC: 25718 AN: 67974

Other (OTH) AF: 0.369 AC: 780 AN: 2114

Alfa AF: 0.334 Hom.: 3476

Bravo AF: 0.361

Asia WGS AF: 0.340 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.91
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11003136; hg19: chr10-54538540; COSMIC: COSV53388008;