rs1503244

Variant names:

• chr2-67997211-T-C
• rs1503244

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 0.117 in 152,182 control chromosomes in the GnomAD database, including 1,175 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 0.12 (1175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 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: 0.117 AC: 17776 AN: 152064 Hom.: 1176 Cov.: 32

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.0704

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.0798

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.117 AC: 17779 AN: 152182 Hom.: 1175 Cov.: 32 AF XY: 0.113 AC XY: 8370 AN XY: 74394

African (AFR) AF: 0.0941 AC: 3905 AN: 41508

American (AMR) AF: 0.0872 AC: 1333 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0704 AC: 244 AN: 3468

East Asian (EAS) AF: 0.0262 AC: 136 AN: 5182

South Asian (SAS) AF: 0.0975 AC: 470 AN: 4822

European-Finnish (FIN) AF: 0.0798 AC: 847 AN: 10608

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10551 AN: 67986

Other (OTH) AF: 0.0904 AC: 191 AN: 2112

Alfa AF: 0.140 Hom.: 2951

Bravo AF: 0.116

Asia WGS AF: 0.0630 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.64
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1503244; hg19: chr2-68224343;