4-109905119-C-T

Variant names:

• chr4-109905119-C-T
• rs17238095

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 0.232 in 151,986 control chromosomes in the GnomAD database, including 4,154 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 (4154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 8 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 = 0.251 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: 0.232 AC: 35187 AN: 151868 Hom.: 4155 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0843

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.232 AC: 35199 AN: 151986 Hom.: 4154 Cov.: 32 AF XY: 0.228 AC XY: 16924 AN XY: 74266

African (AFR) AF: 0.220 AC: 9135 AN: 41444

American (AMR) AF: 0.216 AC: 3302 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3472

East Asian (EAS) AF: 0.0849 AC: 439 AN: 5172

South Asian (SAS) AF: 0.202 AC: 975 AN: 4816

European-Finnish (FIN) AF: 0.234 AC: 2467 AN: 10528

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17281 AN: 67966

Other (OTH) AF: 0.246 AC: 519 AN: 2106

Alfa AF: 0.242 Hom.: 7742

Bravo AF: 0.229

Asia WGS AF: 0.142 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.71
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs17238095; hg19: chr4-110826275;