rs229515

Positions:

• chr22-37180032-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419128.1(ENSG00000235237):​n.209-2397C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,240 control chromosomes in the GnomAD database, including 11,173 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 0.36 (11171 hom., cov: 34)
  • Exomes 𝑓: 0.35 (2 hom.)
• Consequence: ENSG00000235237 ENST00000419128.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509

Genes affected

ENSG00000235237 (HGNC:40300):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000235237	ENST00000419128.1	n.209-2397C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55318 AN: 152074 Hom.: 11134 Cov.: 34

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.383

GnomAD4 exome AF: 0.354 AC: 17 AN: 48 Hom.: 2 AF XY: 0.361 AC XY: 13 AN XY: 36

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.292

Gnomad4 NFE exome AF: 0.300

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.364 AC: 55428 AN: 152192 Hom.: 11171 Cov.: 34 AF XY: 0.367 AC XY: 27285 AN XY: 74396

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.384

Alfa AF: 0.326 Hom.: 2697

Bravo AF: 0.387

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs229515; hg19: chr22-37576072;