rs13002573

Positions:

• chr2-164058698-A-G
• chr2-164058698-A-T

Variant summary

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

The ENST00000429636.1(ENSG00000237844):​n.197-108439T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,156 control chromosomes in the GnomAD database, including 3,505 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 0.20 (3505 hom., cov: 32)
• Consequence: ENST00000429636.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000429636.1	n.197-108439T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31167 AN: 152038 Hom.: 3501 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.205 AC: 31179 AN: 152156 Hom.: 3505 Cov.: 32 AF XY: 0.204 AC XY: 15145 AN XY: 74392

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.209

Alfa AF: 0.224 Hom.: 4012

Bravo AF: 0.205

Asia WGS AF: 0.272 AC: 942 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.57
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13002573; hg19: chr2-164915208;