9-111044802-C-T

Variant names:

• chr9-111044802-C-T
• rs1468758

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 0.231 in 151,872 control chromosomes in the GnomAD database, including 4,665 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 0.23 (4665 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 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: 0.231 AC: 35083 AN: 151752 Hom.: 4666 Cov.: 29

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.231 AC: 35082 AN: 151872 Hom.: 4665 Cov.: 29 AF XY: 0.233 AC XY: 17311 AN XY: 74228

African (AFR) AF: 0.140 AC: 5794 AN: 41462

American (AMR) AF: 0.297 AC: 4536 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1065 AN: 3460

East Asian (EAS) AF: 0.570 AC: 2914 AN: 5112

South Asian (SAS) AF: 0.206 AC: 992 AN: 4812

European-Finnish (FIN) AF: 0.221 AC: 2334 AN: 10542

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16692 AN: 67922

Other (OTH) AF: 0.258 AC: 543 AN: 2106

Alfa AF: 0.249 Hom.: 10064

Bravo AF: 0.235

Asia WGS AF: 0.296 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.4
DANN	Benign	0.59
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1468758; hg19: chr9-113807082;