rs1488902

Positions:

• chr11-89611857-T-C
• chr11-89611857-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 0.382 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.382 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

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.382

Alfa AF: 0.357 Hom.: 23031

Bravo AF: 0.392

Asia WGS AF: 0.359 AC: 1250 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.0
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: rs1488902; hg19: chr11-89345025;