11-38598190-T-G

Position:

• chr11-38598190-T-G

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 0.415 in 151,982 control chromosomes in the GnomAD database, including 14,694 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 0.42 (14694 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

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 (SAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63107 AN: 151866 Hom.: 14675 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.415 AC: 63139 AN: 151982 Hom.: 14694 Cov.: 32 AF XY: 0.426 AC XY: 31660 AN XY: 74270

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.471

Alfa AF: 0.423 Hom.: 1800

Bravo AF: 0.415

Asia WGS AF: 0.596 AC: 2068 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1038254; hg19: chr11-38619740;