11-38598190-T-G

Variant names:

• chr11-38598190-T-G
• rs1038254

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.211 AC: 8733 AN: 41462

American (AMR) AF: 0.606 AC: 9251 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1799 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2893 AN: 5162

South Asian (SAS) AF: 0.677 AC: 3260 AN: 4814

European-Finnish (FIN) AF: 0.456 AC: 4811 AN: 10546

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.455 AC: 30920 AN: 67958

Other (OTH) AF: 0.471 AC: 992 AN: 2108

Alfa AF: 0.415 Hom.: 1822

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
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs1038254; hg19: chr11-38619740;