5-112697347-G-C

Variant names:

• chr5-112697347-G-C
• rs10051624

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 0.41 in 151,218 control chromosomes in the GnomAD database, including 14,922 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 0.41 (14922 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 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: 0.410 AC: 61958 AN: 151100 Hom.: 14920 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.410 AC: 61972 AN: 151218 Hom.: 14922 Cov.: 31 AF XY: 0.413 AC XY: 30446 AN XY: 73772

African (AFR) AF: 0.149 AC: 6154 AN: 41432

American (AMR) AF: 0.574 AC: 8767 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3468

East Asian (EAS) AF: 0.677 AC: 3494 AN: 5162

South Asian (SAS) AF: 0.557 AC: 2688 AN: 4822

European-Finnish (FIN) AF: 0.398 AC: 4020 AN: 10096

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.497 AC: 33644 AN: 67652

Other (OTH) AF: 0.447 AC: 941 AN: 2106

Alfa AF: 0.420 Hom.: 1443

Bravo AF: 0.413

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.47
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10051624; hg19: chr5-112033044;