6-25708782-CTT-CTTT

Variant names:

• chr6-25708782-C-CT
• rs11441045
• ENST00000703602.1:c.703-9986_703-9985insT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000703602.1(ENSG00000290217):​c.703-9986_703-9985insT 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 0.82 (50143 hom., cov: 0)
• Consequence: ENSG00000290217 ENST00000703602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377

Genes affected

ENSG00000290217 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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
ENSG00000290217	ENST00000703602.1	c.703-9986_703-9985insT		intron_variant	Intron 10 of 11			ENSP00000515390.1

Frequencies

GnomAD3 genomes AF: 0.823 AC: 121606 AN: 147768 Hom.: 50129 Cov.: 0

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.823 AC: 121651 AN: 147840 Hom.: 50143 Cov.: 0 AF XY: 0.821 AC XY: 58976 AN XY: 71834

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.855

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.801

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11441045; hg19: chr6-25709010;