rs6717587

Positions:

• chr2-175292322-T-C
• chr2-175292322-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 0.258 in 152,182 control chromosomes in the GnomAD database, including 5,799 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 0.26 (5799 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.175292322T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000229066	ENST00000438963.2	n.247+34734T>C		intron_variant		3
ENSG00000229066	ENST00000444567.1	n.448+821T>C		intron_variant		3
ENSG00000229066	ENST00000653625.1	n.336+821T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39179 AN: 152066 Hom.: 5777 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.258 AC: 39250 AN: 152182 Hom.: 5799 Cov.: 33 AF XY: 0.258 AC XY: 19164 AN XY: 74414

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.266

Alfa AF: 0.177 Hom.: 1234

Bravo AF: 0.273

Asia WGS AF: 0.312 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6717587; hg19: chr2-176157050;