5-40445579-T-C

Variant names:

• chr5-40445579-T-C
• rs11957215

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 12,287 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 (12287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.392 AC: 59597 AN: 151856 Hom.: 12280 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.392 AC: 59636 AN: 151974 Hom.: 12287 Cov.: 32 AF XY: 0.401 AC XY: 29755 AN XY: 74266

African (AFR) AF: 0.425 AC: 17614 AN: 41430

American (AMR) AF: 0.390 AC: 5949 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3470

East Asian (EAS) AF: 0.753 AC: 3879 AN: 5154

South Asian (SAS) AF: 0.548 AC: 2647 AN: 4826

European-Finnish (FIN) AF: 0.425 AC: 4478 AN: 10544

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

European-Non Finnish (NFE) AF: 0.335 AC: 22741 AN: 67964

Other (OTH) AF: 0.370 AC: 781 AN: 2110

Alfa AF: 0.355 Hom.: 27078

Bravo AF: 0.389

Asia WGS AF: 0.612 AC: 2128 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs11957215; hg19: chr5-40445681;