rs1561244

Variant names:

• chr2-72902257-G-A
• rs1561244

Your query was ambiguous. Multiple possible variants found:

• chr2-72902257-G-A
• chr2-72902257-G-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 0.238 in 151,844 control chromosomes in the GnomAD database, including 5,832 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 0.24 (5832 hom., cov: 33)
• Consequence: LOC100419678 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 1 publications found

Genes affected

LOC100419678 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36042 AN: 151726 Hom.: 5809 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0541

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.186

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.238 AC: 36113 AN: 151844 Hom.: 5832 Cov.: 33 AF XY: 0.231 AC XY: 17166 AN XY: 74188

African (AFR) AF: 0.458 AC: 18981 AN: 41450

American (AMR) AF: 0.152 AC: 2327 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3462

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5182

South Asian (SAS) AF: 0.0550 AC: 265 AN: 4818

European-Finnish (FIN) AF: 0.170 AC: 1777 AN: 10450

Middle Eastern (MID) AF: 0.190 AC: 55 AN: 290

European-Non Finnish (NFE) AF: 0.172 AC: 11704 AN: 67902

Other (OTH) AF: 0.206 AC: 434 AN: 2110

Alfa AF: 0.199 Hom.: 763

Bravo AF: 0.245

Asia WGS AF: 0.0640 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.2
DANN	Benign	0.18
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs1561244; hg19: chr2-73129386;