chr9-114779170-T-C

Variant names:

• chr9-114779170-T-C
• rs7860414

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 0.19 in 152,176 control chromosomes in the GnomAD database, including 2,989 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 0.19 (2989 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 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: 0.190 AC: 28940 AN: 152058 Hom.: 2991 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.0369

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.190 AC: 28948 AN: 152176 Hom.: 2989 Cov.: 32 AF XY: 0.187 AC XY: 13903 AN XY: 74374

African (AFR) AF: 0.136 AC: 5637 AN: 41518

American (AMR) AF: 0.154 AC: 2361 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3470

East Asian (EAS) AF: 0.0366 AC: 190 AN: 5186

South Asian (SAS) AF: 0.160 AC: 772 AN: 4824

European-Finnish (FIN) AF: 0.232 AC: 2450 AN: 10576

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15818 AN: 67988

Other (OTH) AF: 0.204 AC: 431 AN: 2112

Alfa AF: 0.219 Hom.: 16370

Bravo AF: 0.182

Asia WGS AF: 0.0980 AC: 344 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.56
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7860414; hg19: chr9-117541450;