5-98419196-G-T

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 0.374 in 151,968 control chromosomes in the GnomAD database, including 10,903 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 0.37 (10903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.761

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.374 AC: 56723 AN: 151850 Hom.: 10889 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.374 AC: 56767 AN: 151968 Hom.: 10903 Cov.: 32 AF XY: 0.377 AC XY: 28006 AN XY: 74272

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.394

Alfa AF: 0.381 Hom.: 6222

Bravo AF: 0.364

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	7.3
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11241318; hg19: chr5-97754900;