rs950206

Variant names:

• chr4-115259399-A-G
• rs950206

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 0.381 in 152,012 control chromosomes in the GnomAD database, including 12,168 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 0.38 (12168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.487 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: 0.381 AC: 57820 AN: 151894 Hom.: 12160 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.381 AC: 57845 AN: 152012 Hom.: 12168 Cov.: 32 AF XY: 0.372 AC XY: 27620 AN XY: 74272

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.392

Alfa AF: 0.443 Hom.: 8300

Bravo AF: 0.384

Asia WGS AF: 0.217 AC: 751 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs950206; hg19: chr4-116180555;