11-57198500-A-G

Position:

• chr11-57198500-A-G

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 0.111 in 152,286 control chromosomes in the GnomAD database, including 1,067 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 0.11 (1067 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.75

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57198500A>G		intergenic_region
LOC105369309	XR_001748217.1	n.1008-3735T>C		intron_variant
LOC105369309	XR_007062670.1	n.1008-3735T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16917 AN: 152168 Hom.: 1070 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.111 AC: 16920 AN: 152286 Hom.: 1067 Cov.: 32 AF XY: 0.111 AC XY: 8287 AN XY: 74456

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0847

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.0928

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.104

Alfa AF: 0.106 Hom.: 536

Bravo AF: 0.120

Asia WGS AF: 0.155 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501365; hg19: chr11-56965974;