rs291111

Positions:

• chr1-206896181-T-C

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 0.0875 in 152,240 control chromosomes in the GnomAD database, including 1,521 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 0.087 (1521 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.206896181T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0874 AC: 13291 AN: 152122 Hom.: 1515 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0735

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

GnomAD4 genome AF: 0.0875 AC: 13320 AN: 152240 Hom.: 1521 Cov.: 32 AF XY: 0.0848 AC XY: 6317 AN XY: 74450

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.0502

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.0225

Gnomad4 SAS AF: 0.0141

Gnomad4 FIN AF: 0.00151

Gnomad4 NFE AF: 0.0162

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0859 Hom.: 271

Bravo AF: 0.0992

Asia WGS AF: 0.0250 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.73
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs291111; hg19: chr1-207069526;