rs1892512

Positions:

• chr6-6978400-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 0.48 in 151,968 control chromosomes in the GnomAD database, including 18,088 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 0.48 (18088 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.6978400A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72843 AN: 151850 Hom.: 18083 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.480 AC: 72893 AN: 151968 Hom.: 18088 Cov.: 31 AF XY: 0.481 AC XY: 35752 AN XY: 74290

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.496

Alfa AF: 0.514 Hom.: 41009

Bravo AF: 0.483

Asia WGS AF: 0.586 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1892512; hg19: chr6-6978633;