rs1998930

Variant names:

• chr6-156583122-A-G
• rs1998930

Your query was ambiguous. Multiple possible variants found:

• chr6-156583122-A-G
• chr6-156583122-A-T

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 0.331 in 151,890 control chromosomes in the GnomAD database, including 9,339 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 0.33 (9339 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50296 AN: 151772 Hom.: 9344 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.331 AC: 50296 AN: 151890 Hom.: 9339 Cov.: 31 AF XY: 0.333 AC XY: 24721 AN XY: 74184

African (AFR) AF: 0.158 AC: 6543 AN: 41440

American (AMR) AF: 0.304 AC: 4647 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1431 AN: 3472

East Asian (EAS) AF: 0.572 AC: 2935 AN: 5132

South Asian (SAS) AF: 0.522 AC: 2506 AN: 4798

European-Finnish (FIN) AF: 0.376 AC: 3960 AN: 10520

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27146 AN: 67936

Other (OTH) AF: 0.347 AC: 732 AN: 2108

Alfa AF: 0.382 Hom.: 49608

Bravo AF: 0.317

Asia WGS AF: 0.450 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1998930; hg19: chr6-156904256;