rs4982270

Positions:

• chr14-35411612-C-G
• chr14-35411612-C-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 0.52 in 152,016 control chromosomes in the GnomAD database, including 20,506 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 0.52 (20506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 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: 0.520 AC: 78969 AN: 151898 Hom.: 20484 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.520 AC: 79035 AN: 152016 Hom.: 20506 Cov.: 32 AF XY: 0.524 AC XY: 38953 AN XY: 74298

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.515

Alfa AF: 0.506 Hom.: 2376

Bravo AF: 0.516

Asia WGS AF: 0.661 AC: 2299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4982270; hg19: chr14-35880818;