11-60114051-G-C

Variant names:

• chr11-60114051-G-C
• rs574695

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 0.378 in 151,974 control chromosomes in the GnomAD database, including 11,425 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 (11425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.53 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: 0.378 AC: 57436 AN: 151856 Hom.: 11423 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.378 AC: 57454 AN: 151974 Hom.: 11425 Cov.: 32 AF XY: 0.375 AC XY: 27877 AN XY: 74284

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.421

Alfa AF: 0.265 Hom.: 631

Bravo AF: 0.372

Asia WGS AF: 0.456 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs574695; hg19: chr11-59881524;