9-107177990-A-G

Variant names:

• chr9-107177990-A-G
• rs4443717

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262

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.

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

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

Gnomad4 AFR AF: 0.879 AC: 0.878685 AN: 0.878685

Gnomad4 AMR AF: 0.569 AC: 0.569313 AN: 0.569313

Gnomad4 ASJ AF: 0.627 AC: 0.626659 AN: 0.626659

Gnomad4 EAS AF: 0.638 AC: 0.637616 AN: 0.637616

Gnomad4 SAS AF: 0.612 AC: 0.611642 AN: 0.611642

Gnomad4 FIN AF: 0.616 AC: 0.615559 AN: 0.615559

Gnomad4 NFE AF: 0.579 AC: 0.57851 AN: 0.57851

Gnomad4 OTH AF: 0.650 AC: 0.650284 AN: 0.650284

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4443717; hg19: chr9-109940271;