chr11-29243432-A-C

Variant names:

• chr11-29243432-A-C
• rs7949185
• ENST00000530960.1:n.296-17621A>C

Variant summary

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

The ENST00000530960.1(ENSG00000254526):​n.296-17621A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,034 control chromosomes in the GnomAD database, including 9,825 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 (9825 hom., cov: 32)
• Consequence: ENSG00000254526 ENST00000530960.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 1 publications found

Genes affected

ENSG00000254526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.398 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
ENSG00000254526	ENST00000530960.1	n.296-17621A>C		intron_variant	Intron 3 of 4	3
ENSG00000254526	ENST00000742293.1	n.216+31667A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54048 AN: 151916 Hom.: 9815 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.356 AC: 54097 AN: 152034 Hom.: 9825 Cov.: 32 AF XY: 0.357 AC XY: 26527 AN XY: 74328

African (AFR) AF: 0.372 AC: 15436 AN: 41480

American (AMR) AF: 0.407 AC: 6214 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3466

East Asian (EAS) AF: 0.153 AC: 786 AN: 5152

South Asian (SAS) AF: 0.339 AC: 1633 AN: 4818

European-Finnish (FIN) AF: 0.412 AC: 4358 AN: 10570

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23404 AN: 67948

Other (OTH) AF: 0.359 AC: 758 AN: 2110

Alfa AF: 0.212 Hom.: 427

Bravo AF: 0.357

Asia WGS AF: 0.286 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.72
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs7949185; hg19: chr11-29264979;