chr5-40302465-G-C

Variant names:

• chr5-40302465-G-C
• rs1564269

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 0.539 in 151,942 control chromosomes in the GnomAD database, including 23,527 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 0.54 (23527 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81828 AN: 151822 Hom.: 23529 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.539 AC: 81840 AN: 151942 Hom.: 23527 Cov.: 32 AF XY: 0.538 AC XY: 39925 AN XY: 74252

African (AFR) AF: 0.350 AC: 14478 AN: 41420

American (AMR) AF: 0.523 AC: 7968 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2534 AN: 3470

East Asian (EAS) AF: 0.365 AC: 1883 AN: 5152

South Asian (SAS) AF: 0.703 AC: 3385 AN: 4816

European-Finnish (FIN) AF: 0.578 AC: 6109 AN: 10574

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43489 AN: 67960

Other (OTH) AF: 0.601 AC: 1266 AN: 2106

Alfa AF: 0.460 Hom.: 1424

Bravo AF: 0.525

Asia WGS AF: 0.576 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.79
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs1564269; hg19: chr5-40302567;