rs198389

Positions:

• chr1-11859214-A-G

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 0.392 in 152,080 control chromosomes in the GnomAD database, including 12,025 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 0.39 (12025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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: 0.392 AC: 59573 AN: 151962 Hom.: 12003 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.392 AC: 59635 AN: 152080 Hom.: 12025 Cov.: 32 AF XY: 0.390 AC XY: 28982 AN XY: 74362

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.397

Alfa AF: 0.410 Hom.: 21874

Bravo AF: 0.383

Asia WGS AF: 0.354 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.090
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs198389; hg19: chr1-11919271; COSMIC: COSV64687424;