9-104317871-TAGACAGACAGAC-TAGACAGAC

Variant names:

• chr9-104317871-TAGAC-T
• rs71992086
• ENST00000745188.1:n.605-113862_605-113859delGTCT

Variant summary

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

The ENST00000745188.1(ENSG00000297079):​n.605-113862_605-113859delGTCT 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 0.25 (4891 hom., cov: 13)
• Consequence: ENSG00000297079 ENST00000745188.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 1 publications found

Genes affected

ENSG00000297079 (HGNC:):

ACMG classification

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

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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
ENSG00000297079	ENST00000745188.1	n.605-113862_605-113859delGTCT		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.253 AC: 36894 AN: 146098 Hom.: 4887 Cov.: 13

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.252 AC: 36907 AN: 146200 Hom.: 4891 Cov.: 13 AF XY: 0.254 AC XY: 18080 AN XY: 71204

African (AFR) AF: 0.185 AC: 7180 AN: 38752

American (AMR) AF: 0.302 AC: 4373 AN: 14488

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 654 AN: 3408

East Asian (EAS) AF: 0.408 AC: 2005 AN: 4910

South Asian (SAS) AF: 0.279 AC: 1270 AN: 4548

European-Finnish (FIN) AF: 0.259 AC: 2585 AN: 9982

Middle Eastern (MID) AF: 0.172 AC: 50 AN: 290

European-Non Finnish (NFE) AF: 0.270 AC: 18052 AN: 66908

Other (OTH) AF: 0.274 AC: 551 AN: 2012

Alfa AF: 0.0911 Hom.: 157

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs71992086; hg19: chr9-107080152;