chr20-11176363-A-T

Variant names:

• chr20-11176363-A-T
• rs6040399
• ENST00000844940.1:n.98+17575A>T

Variant summary

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

The ENST00000844940.1(ENSG00000309883):​n.98+17575A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 151,792 control chromosomes in the GnomAD database, including 36,377 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 0.69 (36377 hom., cov: 32)
• Consequence: ENSG00000309883 ENST00000844940.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 11 publications found

Genes affected

ENSG00000309883 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372528	XR_937260.2	n.168+213T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309883	ENST00000844940.1	n.98+17575A>T		intron_variant	Intron 1 of 1
ENSG00000309883	ENST00000844941.1	n.133+17575A>T		intron_variant	Intron 2 of 2
ENSG00000309883	ENST00000844942.1	n.150-13685A>T		intron_variant	Intron 2 of 3
ENSG00000309883	ENST00000844943.1	n.128-16091A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104499 AN: 151674 Hom.: 36341 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.689 AC: 104585 AN: 151792 Hom.: 36377 Cov.: 32 AF XY: 0.685 AC XY: 50785 AN XY: 74148

African (AFR) AF: 0.702 AC: 29120 AN: 41466

American (AMR) AF: 0.546 AC: 8305 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3468

East Asian (EAS) AF: 0.486 AC: 2471 AN: 5088

South Asian (SAS) AF: 0.691 AC: 3296 AN: 4770

European-Finnish (FIN) AF: 0.716 AC: 7550 AN: 10546

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.721 AC: 48967 AN: 67946

Other (OTH) AF: 0.706 AC: 1490 AN: 2110

Alfa AF: 0.709 Hom.: 21240

Bravo AF: 0.674

Asia WGS AF: 0.603 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.61
PhyloP100		0.094

Splicing

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

Other links and lift over

dbSNP: rs6040399; hg19: chr20-11157011;