5-40458965-A-G

Variant names:

• chr5-40458965-A-G
• rs10941508

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 0.392 in 151,974 control chromosomes in the GnomAD database, including 12,267 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 0.39 (12267 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59524 AN: 151856 Hom.: 12262 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.392 AC: 59561 AN: 151974 Hom.: 12267 Cov.: 32 AF XY: 0.400 AC XY: 29683 AN XY: 74280

African (AFR) AF: 0.416 AC: 17242 AN: 41452

American (AMR) AF: 0.414 AC: 6313 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3464

East Asian (EAS) AF: 0.759 AC: 3925 AN: 5172

South Asian (SAS) AF: 0.522 AC: 2516 AN: 4824

European-Finnish (FIN) AF: 0.426 AC: 4490 AN: 10532

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22733 AN: 67960

Other (OTH) AF: 0.376 AC: 794 AN: 2110

Alfa AF: 0.355 Hom.: 5034

Bravo AF: 0.391

Asia WGS AF: 0.600 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.74
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10941508; hg19: chr5-40459067;