6-25708782-CTT-CT

Variant names:

• chr6-25708782-CT-C
• rs11441045
• ENST00000703602.1:c.703-9985delT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000703602.1(ENSG00000290217):​c.703-9985delT 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 0.0048 (4 hom., cov: 0)
• Consequence: ENSG00000290217 ENST00000703602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 5 publications found

Genes affected

ENSG00000290217 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 4 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703602.1. 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
	ENSG00000290217	ENST00000703602.1		c.703-9985delT		intron	N/A	ENSP00000515390.1	A0A994J4C2

Frequencies

GnomAD3 genomes AF: 0.00481 AC: 711 AN: 147840 Hom.: 4 Cov.: 0

Gnomad AFR AF: 0.00156

Gnomad AMI AF: 0.00221

Gnomad AMR AF: 0.00175

Gnomad ASJ AF: 0.000292

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000214

Gnomad FIN AF: 0.0115

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00748

Gnomad OTH AF: 0.00488

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

GnomAD4 genome AF: 0.00481 AC: 712 AN: 147912 Hom.: 4 Cov.: 0 AF XY: 0.00495 AC XY: 356 AN XY: 71868

African (AFR) AF: 0.00158 AC: 64 AN: 40388

American (AMR) AF: 0.00175 AC: 26 AN: 14880

Ashkenazi Jewish (ASJ) AF: 0.000292 AC: 1 AN: 3422

East Asian (EAS) AF: 0.00 AC: 0 AN: 5060

South Asian (SAS) AF: 0.000215 AC: 1 AN: 4652

European-Finnish (FIN) AF: 0.0115 AC: 108 AN: 9404

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.00748 AC: 500 AN: 66848

Other (OTH) AF: 0.00484 AC: 10 AN: 2064

Alfa AF: 0.00669 Hom.: 1612

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs11441045; hg19: chr6-25709010;