chr14-75374509-C-T

Variant names:

• chr14-75374509-C-T
• rs2205187

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 0.236 in 152,114 control chromosomes in the GnomAD database, including 4,570 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 0.24 (4570 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35820 AN: 151996 Hom.: 4563 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.236 AC: 35834 AN: 152114 Hom.: 4570 Cov.: 32 AF XY: 0.231 AC XY: 17197 AN XY: 74368

African (AFR) AF: 0.337 AC: 13971 AN: 41474

American (AMR) AF: 0.199 AC: 3041 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 678 AN: 3470

East Asian (EAS) AF: 0.0967 AC: 501 AN: 5182

South Asian (SAS) AF: 0.146 AC: 704 AN: 4820

European-Finnish (FIN) AF: 0.200 AC: 2116 AN: 10584

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14097 AN: 67974

Other (OTH) AF: 0.235 AC: 495 AN: 2106

Alfa AF: 0.215 Hom.: 654

Bravo AF: 0.240

Asia WGS AF: 0.121 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.44
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs2205187; hg19: chr14-75841212;