rs9997120

Variant names:

• chr4-146171937-C-T
• rs9997120

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 0.228 in 152,024 control chromosomes in the GnomAD database, including 4,115 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 (4115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.241 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: 0.228 AC: 34689 AN: 151906 Hom.: 4109 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0756

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.228 AC: 34717 AN: 152024 Hom.: 4115 Cov.: 32 AF XY: 0.229 AC XY: 16992 AN XY: 74306

African (AFR) AF: 0.219 AC: 9096 AN: 41454

American (AMR) AF: 0.238 AC: 3639 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3468

East Asian (EAS) AF: 0.0757 AC: 392 AN: 5176

South Asian (SAS) AF: 0.167 AC: 808 AN: 4824

European-Finnish (FIN) AF: 0.273 AC: 2884 AN: 10558

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16593 AN: 67958

Other (OTH) AF: 0.187 AC: 394 AN: 2110

Alfa AF: 0.234 Hom.: 2438

Bravo AF: 0.221

Asia WGS AF: 0.127 AC: 443 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	15
DANN	Benign	0.76
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs9997120; hg19: chr4-147093089; COSMIC: COSV56852795;