rs950206

Variant names:

• chr4-115259399-A-G
• rs950206

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.224 AC: 9311 AN: 41476

American (AMR) AF: 0.431 AC: 6579 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1013 AN: 3462

East Asian (EAS) AF: 0.187 AC: 973 AN: 5190

South Asian (SAS) AF: 0.237 AC: 1141 AN: 4822

European-Finnish (FIN) AF: 0.387 AC: 4088 AN: 10560

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33365 AN: 67928

Other (OTH) AF: 0.392 AC: 827 AN: 2112

Alfa AF: 0.444 Hom.: 9229

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
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs950206; hg19: chr4-116180555;