11-69143386-T-C

Variant names:

• chr11-69143386-T-C
• rs2924538
• ENST00000637084.1:n.*511+7854T>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+7854T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,184 control chromosomes in the GnomAD database, including 6,522 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 0.29 (6522 hom., cov: 33)
• Consequence: ENSG00000287725 ENST00000637084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 3 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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 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+7854T>C		intron_variant	Intron 14 of 14	1		ENSP00000490615.1
ENSG00000287725	ENST00000692585.1	n.*511+7854T>C		intron_variant	Intron 14 of 14			ENSP00000509200.1

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43719 AN: 152066 Hom.: 6510 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.288 AC: 43770 AN: 152184 Hom.: 6522 Cov.: 33 AF XY: 0.286 AC XY: 21290 AN XY: 74408

African (AFR) AF: 0.281 AC: 11648 AN: 41506

American (AMR) AF: 0.273 AC: 4171 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3468

East Asian (EAS) AF: 0.124 AC: 643 AN: 5184

South Asian (SAS) AF: 0.165 AC: 799 AN: 4828

European-Finnish (FIN) AF: 0.322 AC: 3410 AN: 10576

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21093 AN: 68016

Other (OTH) AF: 0.306 AC: 646 AN: 2110

Alfa AF: 0.194 Hom.: 487

Bravo AF: 0.288

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.3
DANN	Benign	0.85
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs2924538; hg19: chr11-68910854;