rs1319462

Positions:

• chr14-61752507-G-A
• chr14-61752507-G-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 0.797 in 152,220 control chromosomes in the GnomAD database, including 48,812 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 0.80 (48812 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 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: 0.797 AC: 121180 AN: 152102 Hom.: 48756 Cov.: 33

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.797 AC: 121301 AN: 152220 Hom.: 48812 Cov.: 33 AF XY: 0.799 AC XY: 59477 AN XY: 74424

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.947

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.788

Alfa AF: 0.822 Hom.: 60968

Bravo AF: 0.787

Asia WGS AF: 0.737 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.015
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1319462; hg19: chr14-62219225;