11-69143111-T-C

Variant names:

• chr11-69143111-T-C
• rs2924540
• ENST00000637084.1:n.*511+7579T>C

Variant summary

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

The ENST00000637084.1(ENSG00000287725):​n.*511+7579T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,096 control chromosomes in the GnomAD database, including 9,154 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 0.34 (9154 hom., cov: 32)
• Consequence: ENSG00000287725 ENST00000637084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 9 publications found

Genes affected

ENSG00000287725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287725	ENST00000637084.1	n.*511+7579T>C		intron_variant	Intron 14 of 14	1		ENSP00000490615.1
ENSG00000287725	ENST00000692585.1	n.*511+7579T>C		intron_variant	Intron 14 of 14			ENSP00000509200.1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52133 AN: 151978 Hom.: 9142 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.343 AC: 52186 AN: 152096 Hom.: 9154 Cov.: 32 AF XY: 0.343 AC XY: 25517 AN XY: 74338

African (AFR) AF: 0.291 AC: 12100 AN: 41510

American (AMR) AF: 0.331 AC: 5060 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3472

East Asian (EAS) AF: 0.400 AC: 2063 AN: 5162

South Asian (SAS) AF: 0.318 AC: 1535 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3627 AN: 10558

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25109 AN: 67978

Other (OTH) AF: 0.384 AC: 813 AN: 2116

Alfa AF: 0.359 Hom.: 38376

Bravo AF: 0.342

Asia WGS AF: 0.402 AC: 1393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.60
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs2924540; hg19: chr11-68910579;