5-118700852-T-C

Variant names:

• chr5-118700852-T-C
• rs10068737

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 0.604 in 152,060 control chromosomes in the GnomAD database, including 30,178 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 0.60 (30178 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 1 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 = 0.944 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91651 AN: 151942 Hom.: 30118 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.604 AC: 91778 AN: 152060 Hom.: 30178 Cov.: 31 AF XY: 0.607 AC XY: 45106 AN XY: 74332

African (AFR) AF: 0.848 AC: 35197 AN: 41510

American (AMR) AF: 0.572 AC: 8727 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1577 AN: 3468

East Asian (EAS) AF: 0.966 AC: 4991 AN: 5166

South Asian (SAS) AF: 0.599 AC: 2889 AN: 4826

European-Finnish (FIN) AF: 0.485 AC: 5124 AN: 10564

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31353 AN: 67946

Other (OTH) AF: 0.565 AC: 1189 AN: 2106

Alfa AF: 0.296 Hom.: 572

Bravo AF: 0.624

Asia WGS AF: 0.741 AC: 2578 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.51
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs10068737; hg19: chr5-118036547;