rs7143973

Positions:

• chr14-41478625-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 0.366 in 151,962 control chromosomes in the GnomAD database, including 10,664 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 0.37 (10664 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 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: 0.366 AC: 55599 AN: 151846 Hom.: 10652 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.366 AC: 55647 AN: 151962 Hom.: 10664 Cov.: 32 AF XY: 0.370 AC XY: 27489 AN XY: 74274

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.347

Alfa AF: 0.389 Hom.: 15242

Bravo AF: 0.361

Asia WGS AF: 0.417 AC: 1440 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.49
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7143973; hg19: chr14-41947828;