rs1375575

Variant names:

• chr14-85274151-T-C
• rs1375575

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 0.593 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.778 AC: 32220 AN: 41406

American (AMR) AF: 0.499 AC: 7581 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1919 AN: 3464

East Asian (EAS) AF: 0.0925 AC: 474 AN: 5124

South Asian (SAS) AF: 0.363 AC: 1751 AN: 4818

European-Finnish (FIN) AF: 0.584 AC: 6155 AN: 10532

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.560 AC: 37995 AN: 67794

Other (OTH) AF: 0.551 AC: 1158 AN: 2102

Alfa AF: 0.594 Hom.: 9285

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
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1375575; hg19: chr14-85740495;