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. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.226 AC: 9368 AN: 41456

American (AMR) AF: 0.320 AC: 4890 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1765 AN: 3466

East Asian (EAS) AF: 0.258 AC: 1333 AN: 5172

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4820

European-Finnish (FIN) AF: 0.336 AC: 3543 AN: 10554

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29853 AN: 67968

Other (OTH) AF: 0.404 AC: 854 AN: 2112

Alfa AF: 0.420 Hom.: 37504

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
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs2353550; hg19: chr1-207146837;