5-106753893-A-G

Variant names:

• chr5-106753893-A-G
• rs1561350

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 0.716 in 151,974 control chromosomes in the GnomAD database, including 39,018 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 0.72 (39018 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.831 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: 0.716 AC: 108725 AN: 151856 Hom.: 38972 Cov.: 31

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.716 AC: 108821 AN: 151974 Hom.: 39018 Cov.: 31 AF XY: 0.720 AC XY: 53457 AN XY: 74274

African (AFR) AF: 0.686 AC: 28456 AN: 41468

American (AMR) AF: 0.768 AC: 11714 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2519 AN: 3468

East Asian (EAS) AF: 0.852 AC: 4393 AN: 5156

South Asian (SAS) AF: 0.754 AC: 3631 AN: 4818

European-Finnish (FIN) AF: 0.717 AC: 7564 AN: 10554

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48211 AN: 67930

Other (OTH) AF: 0.727 AC: 1537 AN: 2114

Alfa AF: 0.698 Hom.: 3575

Bravo AF: 0.719

Asia WGS AF: 0.798 AC: 2778 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	0.39
DANN	Benign	0.35
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1561350; hg19: chr5-106089594; COSMIC: COSV60177488;