chr5-118571597-C-A

Variant names:

• chr5-118571597-C-A
• rs10213999

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 0.401 in 152,144 control chromosomes in the GnomAD database, including 15,947 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 0.40 (15947 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.894
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60851 AN: 152024 Hom.: 15920 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.0353

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.401 AC: 60934 AN: 152144 Hom.: 15947 Cov.: 32 AF XY: 0.390 AC XY: 29017 AN XY: 74370

African (AFR) AF: 0.740 AC: 30707 AN: 41514

American (AMR) AF: 0.265 AC: 4056 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3466

East Asian (EAS) AF: 0.0351 AC: 182 AN: 5178

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4816

European-Finnish (FIN) AF: 0.200 AC: 2118 AN: 10586

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19798 AN: 67978

Other (OTH) AF: 0.394 AC: 833 AN: 2114

Alfa AF: 0.331 Hom.: 13427

Bravo AF: 0.420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.76
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs10213999; hg19: chr5-117907292;