rs1956388

Positions:

• chr14-28663671-G-A
• chr14-28663671-G-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 0.49 in 151,732 control chromosomes in the GnomAD database, including 18,264 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 0.49 (18264 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 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: 0.490 AC: 74236 AN: 151614 Hom.: 18226 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.490 AC: 74332 AN: 151732 Hom.: 18264 Cov.: 32 AF XY: 0.494 AC XY: 36595 AN XY: 74102

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.491

Alfa AF: 0.462 Hom.: 20264

Bravo AF: 0.497

Asia WGS AF: 0.559 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1956388; hg19: chr14-29132877;