rs835154

Variant names:

• chr5-14876460-G-A
• rs835154

Your query was ambiguous. Multiple possible variants found:

• chr5-14876460-G-A
• chr5-14876460-G-C
• chr5-14876460-G-T

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 0.648 in 152,034 control chromosomes in the GnomAD database, including 33,615 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 0.65 (33615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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: 0.648 AC: 98454 AN: 151916 Hom.: 33546 Cov.: 32

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.648 AC: 98590 AN: 152034 Hom.: 33615 Cov.: 32 AF XY: 0.647 AC XY: 48096 AN XY: 74292

African (AFR) AF: 0.877 AC: 36383 AN: 41504

American (AMR) AF: 0.555 AC: 8466 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1866 AN: 3472

East Asian (EAS) AF: 0.683 AC: 3533 AN: 5172

South Asian (SAS) AF: 0.605 AC: 2914 AN: 4816

European-Finnish (FIN) AF: 0.599 AC: 6319 AN: 10550

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37283 AN: 67950

Other (OTH) AF: 0.616 AC: 1297 AN: 2104

Alfa AF: 0.585 Hom.: 43960

Bravo AF: 0.655

Asia WGS AF: 0.671 AC: 2335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	10
DANN	Benign	0.65
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs835154; hg19: chr5-14876569;