rs6902875

Positions:

• chr6-132295933-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 0.436 in 152,056 control chromosomes in the GnomAD database, including 18,987 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 0.44 (18987 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.132295933A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66184 AN: 151938 Hom.: 18934 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.386

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AC XY: 0 AN XY: 0

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.436 AC: 66286 AN: 152056 Hom.: 18987 Cov.: 32 AF XY: 0.429 AC XY: 31892 AN XY: 74320

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.391

Alfa AF: 0.308 Hom.: 10641

Bravo AF: 0.450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6902875; hg19: chr6-132617072; COSMIC: COSV60948306;