rs6758183

Variant names:

• chr2-226136270-G-A
• rs6758183

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 0.192 in 152,172 control chromosomes in the GnomAD database, including 3,228 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 0.19 (3228 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.192 AC: 29160 AN: 152054 Hom.: 3231 Cov.: 33

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0707

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.192 AC: 29153 AN: 152172 Hom.: 3228 Cov.: 33 AF XY: 0.187 AC XY: 13913 AN XY: 74408

Gnomad4 AFR AF: 0.0954

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0707

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.239

Alfa AF: 0.238 Hom.: 5921

Bravo AF: 0.186

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6758183; hg19: chr2-227000986;