rs4981929

Positions:

• chr14-31903446-A-G

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 0.554 in 151,852 control chromosomes in the GnomAD database, including 23,726 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 0.55 (23726 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 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: 0.554 AC: 84098 AN: 151734 Hom.: 23681 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.554 AC: 84199 AN: 151852 Hom.: 23726 Cov.: 31 AF XY: 0.556 AC XY: 41245 AN XY: 74240

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.536

Alfa AF: 0.509 Hom.: 33756

Bravo AF: 0.565

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4981929; hg19: chr14-32372652;