chr9-107177990-A-G

Variant names:

• chr9-107177990-A-G
• rs4443717
• ENST00000807600.1:n.914-7484T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000807600.1(ENSG00000304997):​n.914-7484T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,038 control chromosomes in the GnomAD database, including 35,065 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (35065 hom., cov: 31)
• Consequence: ENSG00000304997 ENST00000807600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 7 publications found

Genes affected

ENSG00000304997 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807600.1. 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
	ENSG00000304997	ENST00000807600.1		n.914-7484T>C		intron	N/A
	ENSG00000304997	ENST00000807601.1		n.322-7484T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101320 AN: 151920 Hom.: 35023 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.667 AC: 101415 AN: 152038 Hom.: 35065 Cov.: 31 AF XY: 0.666 AC XY: 49511 AN XY: 74300

African (AFR) AF: 0.879 AC: 36483 AN: 41520

American (AMR) AF: 0.569 AC: 8690 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2172 AN: 3466

East Asian (EAS) AF: 0.638 AC: 3285 AN: 5152

South Asian (SAS) AF: 0.612 AC: 2942 AN: 4810

European-Finnish (FIN) AF: 0.616 AC: 6504 AN: 10566

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.579 AC: 39304 AN: 67940

Other (OTH) AF: 0.650 AC: 1376 AN: 2116

Alfa AF: 0.598 Hom.: 47382

Bravo AF: 0.672

Asia WGS AF: 0.623 AC: 2165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.33
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs4443717; hg19: chr9-109940271;