rs6040399

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844940.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309883	ENST00000844940.1		n.98+17575A>T		intron	N/A
	ENSG00000309883	ENST00000844941.1		n.133+17575A>T		intron	N/A
	ENSG00000309883	ENST00000844942.1		n.150-13685A>T		intron	N/A

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 v4.9

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;