chr2-10433072-C-T

Variant names:

• chr2-10433072-C-T
• rs11694911
• ENST00000757451.1:n.251+828C>T

Variant summary

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

The ENST00000757451.1(ENSG00000298698):​n.251+828C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 151,606 control chromosomes in the GnomAD database, including 1,267 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 0.12 (1267 hom., cov: 34)
• Consequence: ENSG00000298698 ENST00000757451.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 4 publications found

Genes affected

ENSG00000298698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757451.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298698	ENST00000757451.1		n.251+828C>T		intron	N/A
	ENSG00000298698	ENST00000757452.1		n.132+828C>T		intron	N/A
	ENSG00000298739	ENST00000757688.1		n.-170G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18412 AN: 151486 Hom.: 1265 Cov.: 34

Gnomad AFR AF: 0.0995

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.122 AC: 18421 AN: 151606 Hom.: 1267 Cov.: 34 AF XY: 0.126 AC XY: 9372 AN XY: 74120

African (AFR) AF: 0.0996 AC: 4075 AN: 40902

American (AMR) AF: 0.118 AC: 1812 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 418 AN: 3470

East Asian (EAS) AF: 0.330 AC: 1706 AN: 5164

South Asian (SAS) AF: 0.180 AC: 869 AN: 4832

European-Finnish (FIN) AF: 0.167 AC: 1773 AN: 10614

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7273 AN: 68016

Other (OTH) AF: 0.115 AC: 242 AN: 2110

Alfa AF: 0.113 Hom.: 3042

Bravo AF: 0.115

Asia WGS AF: 0.237 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.47
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs11694911; hg19: chr2-10573198;