rs11781101

Positions:

• chr8-139235419-T-C

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 0.39 in 152,004 control chromosomes in the GnomAD database, including 11,770 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 0.39 (11770 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 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: 0.390 AC: 59270 AN: 151886 Hom.: 11756 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.390 AC: 59308 AN: 152004 Hom.: 11770 Cov.: 32 AF XY: 0.394 AC XY: 29256 AN XY: 74326

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.362

Alfa AF: 0.404 Hom.: 25163

Bravo AF: 0.387

Asia WGS AF: 0.288 AC: 1007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11781101; hg19: chr8-140247662;