chr11-4570509-T-G

Position:

• chr11-4570509-T-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 0.618 in 142,552 control chromosomes in the GnomAD database, including 27,457 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 0.62 (27457 hom., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.4570509T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.618 AC: 88103 AN: 142486 Hom.: 27444 Cov.: 22

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.618 AC: 88142 AN: 142552 Hom.: 27457 Cov.: 22 AF XY: 0.617 AC XY: 42475 AN XY: 68820

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.614

Alfa AF: 0.587 Hom.: 22756

Bravo AF: 0.621

Asia WGS AF: 0.732 AC: 2505 AN: 3422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10768096; hg19: chr11-4591739;