rs1998930

chr6-156583122-A-Gchr6-156583122-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;