rs1451610

Variant names:

• chr11-88250425-A-T
• rs1451610

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 152,046 control chromosomes in the GnomAD database, including 12,063 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 (12063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.474 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: 59323 AN: 151928 Hom.: 12059 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.390 AC: 59341 AN: 152046 Hom.: 12063 Cov.: 32 AF XY: 0.393 AC XY: 29225 AN XY: 74308

African (AFR) AF: 0.291 AC: 12047 AN: 41462

American (AMR) AF: 0.483 AC: 7370 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1514 AN: 3470

East Asian (EAS) AF: 0.393 AC: 2037 AN: 5182

South Asian (SAS) AF: 0.387 AC: 1867 AN: 4822

European-Finnish (FIN) AF: 0.453 AC: 4780 AN: 10544

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28557 AN: 67988

Other (OTH) AF: 0.373 AC: 788 AN: 2114

Alfa AF: 0.400 Hom.: 1565

Bravo AF: 0.392

Asia WGS AF: 0.361 AC: 1249 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.26
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs1451610; hg19: chr11-87983593;