9-107700649-C-T

Variant names:

• chr9-107700649-C-T
• rs2149998

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 0.71 in 152,124 control chromosomes in the GnomAD database, including 39,164 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 0.71 (39164 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 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: 0.710 AC: 107938 AN: 152006 Hom.: 39108 Cov.: 33

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.710 AC: 108053 AN: 152124 Hom.: 39164 Cov.: 33 AF XY: 0.711 AC XY: 52826 AN XY: 74330

African (AFR) AF: 0.825 AC: 34268 AN: 41536

American (AMR) AF: 0.773 AC: 11827 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2565 AN: 3472

East Asian (EAS) AF: 0.839 AC: 4329 AN: 5158

South Asian (SAS) AF: 0.740 AC: 3574 AN: 4830

European-Finnish (FIN) AF: 0.560 AC: 5905 AN: 10548

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43030 AN: 67970

Other (OTH) AF: 0.726 AC: 1535 AN: 2114

Alfa AF: 0.671 Hom.: 57084

Bravo AF: 0.731

Asia WGS AF: 0.765 AC: 2660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.47
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs2149998; hg19: chr9-110462930;