6-113150316-A-T

Variant names:

• chr6-113150316-A-T
• rs1115620
• ENST00000722487.1:n.140-23030A>T

Variant summary

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

The ENST00000722487.1(ENSG00000287728):​n.140-23030A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,874 control chromosomes in the GnomAD database, including 14,329 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 0.43 (14329 hom., cov: 32)
• Consequence: ENSG00000287728 ENST00000722487.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 1 publications found

Genes affected

ENSG00000287728 (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 (AFR) allele frequency at 95% confidence interval = 0.486 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
ENSG00000287728	ENST00000722487.1	n.140-23030A>T		intron_variant	Intron 1 of 2
ENSG00000287728	ENST00000722488.1	n.436+12521A>T		intron_variant	Intron 2 of 6
ENSG00000287728	ENST00000722489.1	n.83-23030A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65280 AN: 151756 Hom.: 14315 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.435

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.430 AC: 65338 AN: 151874 Hom.: 14329 Cov.: 32 AF XY: 0.433 AC XY: 32153 AN XY: 74212

African (AFR) AF: 0.492 AC: 20356 AN: 41416

American (AMR) AF: 0.407 AC: 6202 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1483 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2490 AN: 5144

South Asian (SAS) AF: 0.329 AC: 1584 AN: 4812

European-Finnish (FIN) AF: 0.488 AC: 5157 AN: 10564

Middle Eastern (MID) AF: 0.438 AC: 126 AN: 288

European-Non Finnish (NFE) AF: 0.395 AC: 26798 AN: 67928

Other (OTH) AF: 0.437 AC: 922 AN: 2108

Alfa AF: 0.289 Hom.: 727

Bravo AF: 0.431

Asia WGS AF: 0.391 AC: 1363 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	2.7
DANN	Benign	0.73
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1115620; hg19: chr6-113471518;