rs2353550

Variant names:

• chr1-206973492-A-G
• rs2353550

Your query was ambiguous. Multiple possible variants found:

• chr1-206973492-A-G
• chr1-206973492-A-T

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 0.35 in 152,016 control chromosomes in the GnomAD database, including 10,099 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 0.35 (10099 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

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 (NFE) allele frequency at 95% confidence interval = 0.435 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: 0.350 AC: 53167 AN: 151898 Hom.: 10098 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.350 AC: 53190 AN: 152016 Hom.: 10099 Cov.: 31 AF XY: 0.341 AC XY: 25347 AN XY: 74290

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.404

Alfa AF: 0.426 Hom.: 26218

Bravo AF: 0.343

Asia WGS AF: 0.231 AC: 806 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	1.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2353550; hg19: chr1-207146837;