rs74090038

Variant names:

• chr14-104796444-C-T
• rs74090038

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.283 in 152,080 control chromosomes in the GnomAD database, including 6,390 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 0.28 (6390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 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: 0.283 AC: 43015 AN: 151962 Hom.: 6382 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.283 AC: 43053 AN: 152080 Hom.: 6390 Cov.: 32 AF XY: 0.280 AC XY: 20811 AN XY: 74324

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.270

Alfa AF: 0.290 Hom.: 900

Bravo AF: 0.281

Asia WGS AF: 0.133 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74090038; hg19: chr14-105262781;