9-104317871-TAGACAGACAGAC-TAGAC

Variant names:

• chr9-104317871-TAGACAGAC-T
• rs71992086
• ENST00000745188.1:n.605-113866_605-113859delGTCTGTCT

Variant summary

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

The ENST00000745188.1(ENSG00000297079):​n.605-113866_605-113859delGTCTGTCT 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 0.017 (62 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 (AFR) allele frequency at 95% confidence interval = 0.0566 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.605-113866_605-113859delGTCTGTCT		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.0168 AC: 2468 AN: 146920 Hom.: 63 Cov.: 13

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00610

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00301

Gnomad SAS AF: 0.00391

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00321

Gnomad NFE AF: 0.000773

Gnomad OTH AF: 0.0115

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

GnomAD4 genome AF: 0.0169 AC: 2479 AN: 147024 Hom.: 62 Cov.: 13 AF XY: 0.0164 AC XY: 1173 AN XY: 71666

African (AFR) AF: 0.0586 AC: 2280 AN: 38906

American (AMR) AF: 0.00609 AC: 89 AN: 14606

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3424

East Asian (EAS) AF: 0.00302 AC: 15 AN: 4968

South Asian (SAS) AF: 0.00391 AC: 18 AN: 4598

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10064

Middle Eastern (MID) AF: 0.00690 AC: 2 AN: 290

European-Non Finnish (NFE) AF: 0.000773 AC: 52 AN: 67232

Other (OTH) AF: 0.0113 AC: 23 AN: 2030

Alfa AF: 0.000240 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;