2-19429543-T-C

Position:

• chr2-19429543-T-C

Variant summary

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

The XR_939779.3(LOC101928196):​n.527+20468A>G 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 0.217 in 152,200 control chromosomes in the GnomAD database, including 4,854 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 0.22 (4854 hom., cov: 33)
• Consequence: LOC101928196 XR_939779.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496

Genes affected

LOC101928196 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928196	XR_939779.3	n.527+20468A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33034 AN: 152082 Hom.: 4851 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.217 AC: 33052 AN: 152200 Hom.: 4854 Cov.: 33 AF XY: 0.222 AC XY: 16520 AN XY: 74418

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.239

Alfa AF: 0.164 Hom.: 2532

Bravo AF: 0.238

Asia WGS AF: 0.492 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	9.2
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13398721; hg19: chr2-19629304;