5-38250903-G-A

Position:

• chr5-38250903-G-A

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 0.248 in 151,812 control chromosomes in the GnomAD database, including 5,394 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 0.25 (5394 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37646 AN: 151694 Hom.: 5401 Cov.: 31

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.248 AC: 37632 AN: 151812 Hom.: 5394 Cov.: 31 AF XY: 0.246 AC XY: 18284 AN XY: 74180

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.266

Alfa AF: 0.304 Hom.: 10086

Bravo AF: 0.243

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6867736; hg19: chr5-38251005;