11-60169506-A-G

Variant names:

• chr11-60169506-A-G
• rs667897

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 0.449 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
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.472 AC: 19563 AN: 41436

American (AMR) AF: 0.365 AC: 5584 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1727 AN: 3472

East Asian (EAS) AF: 0.370 AC: 1917 AN: 5180

South Asian (SAS) AF: 0.580 AC: 2787 AN: 4802

European-Finnish (FIN) AF: 0.346 AC: 3655 AN: 10562

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31398 AN: 67968

Other (OTH) AF: 0.472 AC: 995 AN: 2110

Alfa AF: 0.454 Hom.: 27934

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs667897; hg19: chr11-59936979;