rs667897

Variant names:

• chr11-60169506-A-G
• rs667897

Your query was ambiguous. Multiple possible variants found:

• chr11-60169506-A-G
• chr11-60169506-A-T

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 0.449 in 152,020 control chromosomes in the GnomAD database, including 15,489 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 0.45 (15489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.562 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: 0.448 AC: 68117 AN: 151902 Hom.: 15466 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.449 AC: 68182 AN: 152020 Hom.: 15489 Cov.: 32 AF XY: 0.444 AC XY: 33019 AN XY: 74324

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.472

Alfa AF: 0.260 Hom.: 428

Bravo AF: 0.446

Asia WGS AF: 0.477 AC: 1659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.4
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs667897; hg19: chr11-59936979;