rs1998394

Variant names:

• chr6-165251364-C-T
• rs1998394

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 0.403 in 151,968 control chromosomes in the GnomAD database, including 13,462 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 0.40 (13462 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.403 AC: 61121 AN: 151850 Hom.: 13427 Cov.: 31

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.403 AC: 61206 AN: 151968 Hom.: 13462 Cov.: 31 AF XY: 0.403 AC XY: 29937 AN XY: 74248

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.357

Alfa AF: 0.341 Hom.: 12220

Bravo AF: 0.402

Asia WGS AF: 0.295 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1998394; hg19: chr6-165664853;