rs1892512

Variant names:

• chr6-6978400-A-G
• rs1892512

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.373 AC: 15467 AN: 41446

American (AMR) AF: 0.564 AC: 8610 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2189 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3374 AN: 5164

South Asian (SAS) AF: 0.528 AC: 2542 AN: 4814

European-Finnish (FIN) AF: 0.423 AC: 4459 AN: 10548

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34499 AN: 67938

Other (OTH) AF: 0.496 AC: 1047 AN: 2110

Alfa AF: 0.508 Hom.: 84662

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
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1892512; hg19: chr6-6978633;