rs2209544

Positions:

• chr6-24157147-C-A

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 0.0839 in 152,164 control chromosomes in the GnomAD database, including 703 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 0.084 (703 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.24157147C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0840 AC: 12765 AN: 152046 Hom.: 705 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0553

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0929

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

GnomAD4 genome AF: 0.0839 AC: 12767 AN: 152164 Hom.: 703 Cov.: 32 AF XY: 0.0853 AC XY: 6347 AN XY: 74390

Gnomad4 AFR AF: 0.0255

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0553

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0948

Alfa AF: 0.101 Hom.: 1709

Bravo AF: 0.0814

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.14
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2209544; hg19: chr6-24157375;