5-120862616-G-A

Variant names:

• chr5-120862616-G-A
• rs10041997

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 0.485 in 151,820 control chromosomes in the GnomAD database, including 17,907 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 0.49 (17907 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.554 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: 0.485 AC: 73586 AN: 151698 Hom.: 17854 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.485 AC: 73703 AN: 151820 Hom.: 17907 Cov.: 32 AF XY: 0.491 AC XY: 36433 AN XY: 74192

African (AFR) AF: 0.510 AC: 21094 AN: 41394

American (AMR) AF: 0.535 AC: 8149 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1633 AN: 3466

East Asian (EAS) AF: 0.544 AC: 2801 AN: 5148

South Asian (SAS) AF: 0.571 AC: 2734 AN: 4784

European-Finnish (FIN) AF: 0.486 AC: 5117 AN: 10526

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30590 AN: 67944

Other (OTH) AF: 0.477 AC: 1006 AN: 2110

Alfa AF: 0.463 Hom.: 50915

Bravo AF: 0.488

Asia WGS AF: 0.572 AC: 1986 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.023
DANN	Benign	0.47
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10041997; hg19: chr5-120198311;