5-38192509-G-C

Variant names:

• chr5-38192509-G-C
• rs9292700

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0392

Gnomad4 ASJ AF: 0.0236

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0403

Gnomad4 NFE AF: 0.0258

Gnomad4 OTH AF: 0.0553

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9292700; hg19: chr5-38192611;