17-40859506-AT-ATT

Variant names:

• chr17-40859506-A-AT
• rs11371001
• ENST00000579136.1:n.62-3580_62-3579insT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000579136.1(ENSG00000265359):​n.62-3580_62-3579insT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.84 (54064 hom., cov: 0)
• Consequence: ENSG00000265359 ENST00000579136.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.761
• Publications: 1 publications found

Genes affected

ENSG00000265359 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579136.1. 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
	ENSG00000265359	ENST00000579136.1	TSL:3	n.62-3580_62-3579insT		intron	N/A
	ENSG00000265359	ENST00000818906.1		n.61+8646_61+8647insT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.844 AC: 126831 AN: 150304 Hom.: 54015 Cov.: 0

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.844 AC: 126935 AN: 150420 Hom.: 54064 Cov.: 0 AF XY: 0.844 AC XY: 61970 AN XY: 73390

African (AFR) AF: 0.961 AC: 39304 AN: 40886

American (AMR) AF: 0.846 AC: 12761 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2798 AN: 3466

East Asian (EAS) AF: 0.958 AC: 4891 AN: 5108

South Asian (SAS) AF: 0.796 AC: 3758 AN: 4724

European-Finnish (FIN) AF: 0.773 AC: 7949 AN: 10288

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 52678 AN: 67566

Other (OTH) AF: 0.829 AC: 1733 AN: 2090

Alfa AF: 0.723 Hom.: 1423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.76

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11371001;

hg19: chr17-39015758;