rs1475035

Variant names:

• chr14-68871507-C-T
• rs1475035

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 0.297 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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

African (AFR) AF: 0.284 AC: 11774 AN: 41474

American (AMR) AF: 0.222 AC: 3399 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3472

East Asian (EAS) AF: 0.496 AC: 2561 AN: 5160

South Asian (SAS) AF: 0.250 AC: 1206 AN: 4824

European-Finnish (FIN) AF: 0.334 AC: 3524 AN: 10566

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20828 AN: 67964

Other (OTH) AF: 0.295 AC: 621 AN: 2108

Alfa AF: 0.300 Hom.: 4285

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1475035; hg19: chr14-69338224;