rs1475035

Variant names:

• chr14-68871507-C-T
• rs1475035

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 0.297 in 152,062 control chromosomes in the GnomAD database, including 6,905 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 0.30 (6905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 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: 0.297 AC: 45197 AN: 151942 Hom.: 6898 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.297 AC: 45223 AN: 152062 Hom.: 6905 Cov.: 32 AF XY: 0.297 AC XY: 22084 AN XY: 74328

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.295

Alfa AF: 0.301 Hom.: 3875

Bravo AF: 0.290

Asia WGS AF: 0.291 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1475035; hg19: chr14-69338224;