11-114368343-A-G

Variant names:

• chr11-114368343-A-G
• rs10502182
• ENST00000534904.2:n.305-4176T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000534904.2(ENSG00000256195):​n.305-4176T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,062 control chromosomes in the GnomAD database, including 11,510 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 0.37 (11510 hom., cov: 32)
• Consequence: ENSG00000256195 ENST00000534904.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.632

Genes affected

ENSG00000256195 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928940	NR_120567.1	n.299-4176T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256195	ENST00000534904.2	n.305-4176T>C		intron_variant	Intron 2 of 2	1
ENSG00000256195	ENST00000658199.1	n.353-4176T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56079 AN: 151946 Hom.: 11501 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.369 AC: 56120 AN: 152062 Hom.: 11510 Cov.: 32 AF XY: 0.370 AC XY: 27496 AN XY: 74332

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.403

Alfa AF: 0.423 Hom.: 6376

Bravo AF: 0.361

Asia WGS AF: 0.407 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502182; hg19: chr11-114239065;