chr11-89611857-T-C

Variant names:

• chr11-89611857-T-C
• rs1488902

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 0.382 in 151,976 control chromosomes in the GnomAD database, including 11,607 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 0.38 (11607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58029 AN: 151858 Hom.: 11599 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.382 AC: 58070 AN: 151976 Hom.: 11607 Cov.: 32 AF XY: 0.374 AC XY: 27749 AN XY: 74262

African (AFR) AF: 0.498 AC: 20662 AN: 41460

American (AMR) AF: 0.314 AC: 4780 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3470

East Asian (EAS) AF: 0.457 AC: 2355 AN: 5148

South Asian (SAS) AF: 0.283 AC: 1364 AN: 4816

European-Finnish (FIN) AF: 0.235 AC: 2494 AN: 10594

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24136 AN: 67930

Other (OTH) AF: 0.382 AC: 805 AN: 2110

Alfa AF: 0.365 Hom.: 37181

Bravo AF: 0.392

Asia WGS AF: 0.359 AC: 1250 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.0
DANN	Benign	0.87
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1488902; hg19: chr11-89345025;