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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.331 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

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.347

Alfa AF: 0.393 Hom.: 24857

Bravo AF: 0.317

Asia WGS AF: 0.450 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1998930; hg19: chr6-156904256;