5-38192509-G-C

Variant names:

• chr5-38192509-G-C
• rs9292700

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 0.0652 in 152,240 control chromosomes in the GnomAD database, including 564 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 0.065 (564 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 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: 0.0652 AC: 9919 AN: 152122 Hom.: 561 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0403

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0652 AC: 9929 AN: 152240 Hom.: 564 Cov.: 32 AF XY: 0.0667 AC XY: 4964 AN XY: 74432

African (AFR) AF: 0.139 AC: 5755 AN: 41514

American (AMR) AF: 0.0392 AC: 599 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0236 AC: 82 AN: 3472

East Asian (EAS) AF: 0.111 AC: 577 AN: 5176

South Asian (SAS) AF: 0.112 AC: 542 AN: 4818

European-Finnish (FIN) AF: 0.0403 AC: 428 AN: 10610

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0258 AC: 1752 AN: 68032

Other (OTH) AF: 0.0553 AC: 117 AN: 2114

Alfa AF: 0.0192 Hom.: 13

Bravo AF: 0.0672

Asia WGS AF: 0.109 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.69
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9292700; hg19: chr5-38192611;