5-98419196-G-T

Variant names:

• chr5-98419196-G-T
• rs11241318

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;