5-1300314-T-G

Variant names:

• chr5-1300314-T-G
• rs2735946

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 0.756 in 152,066 control chromosomes in the GnomAD database, including 43,868 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 0.76 (43868 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 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: 0.756 AC: 114869 AN: 151948 Hom.: 43822 Cov.: 31

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.756 AC: 114971 AN: 152066 Hom.: 43868 Cov.: 31 AF XY: 0.758 AC XY: 56325 AN XY: 74326

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.906

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.741

Alfa AF: 0.722 Hom.: 13043

Bravo AF: 0.767

Asia WGS AF: 0.882 AC: 3064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2735946; hg19: chr5-1300429;