rs1956397

Variant names:

• chr14-28623484-C-T
• rs1956397

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 0.304 in 151,890 control chromosomes in the GnomAD database, including 7,312 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 (7312 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.417 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: 0.304 AC: 46127 AN: 151772 Hom.: 7294 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.304 AC: 46179 AN: 151890 Hom.: 7312 Cov.: 32 AF XY: 0.308 AC XY: 22845 AN XY: 74206

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.325

Alfa AF: 0.300 Hom.: 1044

Bravo AF: 0.313

Asia WGS AF: 0.372 AC: 1296 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1956397; hg19: chr14-29092690;