rs1675090

chr11-62172634-G-Achr11-62172634-G-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 0.543 in 151,304 control chromosomes in the GnomAD database, including 22,755 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 0.54 (22755 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 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: 0.543 AC: 82119 AN: 151198 Hom.: 22738 Cov.: 30

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.543 AC: 82182 AN: 151304 Hom.: 22755 Cov.: 30 AF XY: 0.538 AC XY: 39746 AN XY: 73860

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.538

Alfa AF: 0.523 Hom.: 41667

Bravo AF: 0.554

Asia WGS AF: 0.525 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	15
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1675090; hg19: chr11-61940106;