chr11-30747131-C-T

Variant names:

• chr11-30747131-C-T
• rs10767873
• ENST00000839775.1:n.462+696C>T

Variant summary

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

The ENST00000839775.1(ENSG00000309240):​n.462+696C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,894 control chromosomes in the GnomAD database, including 11,420 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 (11420 hom., cov: 32)
• Consequence: ENSG00000309240 ENST00000839775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279
• Publications: 15 publications found

Genes affected

ENSG00000309240 (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 (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928338	XR_007062640.1	n.249+5545C>T		intron_variant	Intron 2 of 4
LOC101928338	XR_242862.5	n.249+5545C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309240	ENST00000839775.1	n.462+696C>T		intron_variant	Intron 4 of 4
ENSG00000309240	ENST00000839776.1	n.501+696C>T		intron_variant	Intron 5 of 5
ENSG00000309240	ENST00000839777.1	n.506+696C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54212 AN: 151776 Hom.: 11424 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.357 AC: 54211 AN: 151894 Hom.: 11420 Cov.: 32 AF XY: 0.358 AC XY: 26551 AN XY: 74228

African (AFR) AF: 0.129 AC: 5338 AN: 41464

American (AMR) AF: 0.429 AC: 6532 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3468

East Asian (EAS) AF: 0.351 AC: 1802 AN: 5140

South Asian (SAS) AF: 0.274 AC: 1318 AN: 4810

European-Finnish (FIN) AF: 0.492 AC: 5185 AN: 10532

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31213 AN: 67946

Other (OTH) AF: 0.383 AC: 806 AN: 2106

Alfa AF: 0.423 Hom.: 41942

Bravo AF: 0.344

Asia WGS AF: 0.322 AC: 1119 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.6
DANN	Benign	0.54
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs10767873; hg19: chr11-30768678;