rs1998394

Positions:

• chr6-165251364-C-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 0.403 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;