rs1003223

Variant names:

• chr15-37247606-T-C
• rs1003223

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 0.34 in 152,032 control chromosomes in the GnomAD database, including 10,118 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 0.34 (10118 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 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: 0.340 AC: 51677 AN: 151914 Hom.: 10108 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.340 AC: 51720 AN: 152032 Hom.: 10118 Cov.: 33 AF XY: 0.332 AC XY: 24685 AN XY: 74324

African (AFR) AF: 0.210 AC: 8703 AN: 41492

American (AMR) AF: 0.309 AC: 4722 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1287 AN: 3468

East Asian (EAS) AF: 0.0191 AC: 99 AN: 5180

South Asian (SAS) AF: 0.168 AC: 808 AN: 4808

European-Finnish (FIN) AF: 0.384 AC: 4049 AN: 10552

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30884 AN: 67948

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.376 Hom.: 2343

Bravo AF: 0.330

Asia WGS AF: 0.141 AC: 495 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	4.6
DANN	Benign	0.70
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1003223; hg19: chr15-37539807;