rs11781101

Variant names:

• chr8-139235419-T-C
• rs11781101

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 0.39 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
• Publications: 5 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.324 AC: 13448 AN: 41468

American (AMR) AF: 0.480 AC: 7325 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1350 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1282 AN: 5170

South Asian (SAS) AF: 0.331 AC: 1598 AN: 4828

European-Finnish (FIN) AF: 0.465 AC: 4908 AN: 10560

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.416 AC: 28275 AN: 67942

Other (OTH) AF: 0.362 AC: 761 AN: 2102

Alfa AF: 0.403 Hom.: 52687

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
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs11781101; hg19: chr8-140247662;