5-1300314-T-G

Variant names:

• chr5-1300314-T-G
• rs2735946

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.833 AC: 34560 AN: 41484

American (AMR) AF: 0.781 AC: 11938 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2280 AN: 3468

East Asian (EAS) AF: 0.906 AC: 4666 AN: 5148

South Asian (SAS) AF: 0.857 AC: 4135 AN: 4824

European-Finnish (FIN) AF: 0.662 AC: 7013 AN: 10586

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48077 AN: 67960

Other (OTH) AF: 0.741 AC: 1560 AN: 2104

Alfa AF: 0.724 Hom.: 27663

Bravo AF: 0.767

Asia WGS AF: 0.882 AC: 3064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.39
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2735946; hg19: chr5-1300429;