rs1375575

Positions:

• chr14-85274151-T-C

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 0.593 in 151,644 control chromosomes in the GnomAD database, including 28,238 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 0.59 (28238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89779 AN: 151526 Hom.: 28204 Cov.: 32

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.0923

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.593 AC: 89868 AN: 151644 Hom.: 28238 Cov.: 32 AF XY: 0.585 AC XY: 43348 AN XY: 74064

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.0925

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.551

Alfa AF: 0.595 Hom.: 5404

Bravo AF: 0.594

Asia WGS AF: 0.263 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1375575; hg19: chr14-85740495;