rs1956923

chr14-24508761-G-Achr14-24508761-G-T

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 0.301 in 151,970 control chromosomes in the GnomAD database, including 7,373 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 (7370 hom., cov: 32)
  • Exomes 𝑓: 0.31 (3 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45716 AN: 151804 Hom.: 7357 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.319

GnomAD4 exome AF: 0.313 AC: 15 AN: 48 Hom.: 3 AF XY: 0.269 AC XY: 7 AN XY: 26

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.262

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.301 AC: 45764 AN: 151922 Hom.: 7370 Cov.: 32 AF XY: 0.311 AC XY: 23078 AN XY: 74240

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.318

Alfa AF: 0.271 Hom.: 1344

Bravo AF: 0.313

Asia WGS AF: 0.380 AC: 1323 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.9
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1956923; hg19: chr14-24977967;