rs41463644

Variant names:

• chr14-88945090-A-T
• rs41463644

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 0.26 in 152,056 control chromosomes in the GnomAD database, including 5,431 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 0.26 (5431 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 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: 0.260 AC: 39461 AN: 151938 Hom.: 5424 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.260 AC: 39483 AN: 152056 Hom.: 5431 Cov.: 32 AF XY: 0.256 AC XY: 19063 AN XY: 74352

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.295

Alfa AF: 0.279 Hom.: 773

Bravo AF: 0.257

Asia WGS AF: 0.233 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
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: rs41463644; hg19: chr14-89411434;