chr14-31903446-A-G

Variant names:

• chr14-31903446-A-G
• rs4981929

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;