11-6722659-C-T

Variant names:

• chr11-6722659-C-T
• rs7942744
• ENST00000526769.4:n.147-777G>A

Variant summary

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

The ENST00000526769.4(ENSG00000291143):​n.147-777G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,010 control chromosomes in the GnomAD database, including 22,818 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 0.55 (22818 hom., cov: 31)
• Consequence: ENSG00000291143 ENST00000526769.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 4 publications found

Genes affected

ENSG00000291143 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 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
ENSG00000291143	ENST00000526769.4	n.147-777G>A		intron_variant	Intron 1 of 1	1
ENSG00000294763	ENST00000725824.1	n.218-25518C>T		intron_variant	Intron 1 of 1
ENSG00000294763	ENST00000725825.1	n.231-19695C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82839 AN: 151892 Hom.: 22809 Cov.: 31

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.545 AC: 82886 AN: 152010 Hom.: 22818 Cov.: 31 AF XY: 0.546 AC XY: 40572 AN XY: 74296

African (AFR) AF: 0.516 AC: 21399 AN: 41468

American (AMR) AF: 0.461 AC: 7027 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1947 AN: 3472

East Asian (EAS) AF: 0.641 AC: 3317 AN: 5174

South Asian (SAS) AF: 0.483 AC: 2322 AN: 4812

European-Finnish (FIN) AF: 0.627 AC: 6615 AN: 10550

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38395 AN: 67972

Other (OTH) AF: 0.533 AC: 1124 AN: 2110

Alfa AF: 0.551 Hom.: 64139

Bravo AF: 0.531

Asia WGS AF: 0.481 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.50
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7942744; hg19: chr11-6743890;