rs6937506

Positions:

• chr6-132578260-G-A
• chr6-132578260-G-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 0.251 in 152,016 control chromosomes in the GnomAD database, including 5,447 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 0.25 (5447 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.132578260G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38040 AN: 151896 Hom.: 5434 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.251 AC: 38098 AN: 152016 Hom.: 5447 Cov.: 32 AF XY: 0.248 AC XY: 18446 AN XY: 74302

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.231

Alfa AF: 0.227 Hom.: 981

Bravo AF: 0.258

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6937506; hg19: chr6-132899399;