rs574700

chr11-60088010-C-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 0.0856 in 152,214 control chromosomes in the GnomAD database, including 1,227 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 0.086 (1227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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: 0.0855 AC: 12999 AN: 152096 Hom.: 1221 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0402

Gnomad ASJ AF: 0.0791

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.0697

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

GnomAD4 genome AF: 0.0856 AC: 13026 AN: 152214 Hom.: 1227 Cov.: 32 AF XY: 0.0826 AC XY: 6149 AN XY: 74438

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.0402

Gnomad4 ASJ AF: 0.0791

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.0213

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0340 Hom.: 431

Bravo AF: 0.0945

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.5
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs574700; hg19: chr11-59855483;