chr2-239783349-C-T

Position:

• chr2-239783349-C-T

Variant summary

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

The NR_037808.1(LOC150935):​n.195+2924C>T 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 0.121 in 152,198 control chromosomes in the GnomAD database, including 1,167 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 (1167 hom., cov: 33)
• Consequence: LOC150935 NR_037808.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC150935	NR_037808.1	n.195+2924C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000407524.1	n.195+2924C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18358 AN: 152078 Hom.: 1168 Cov.: 33

Gnomad AFR AF: 0.0857

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.121 AC: 18358 AN: 152198 Hom.: 1167 Cov.: 33 AF XY: 0.124 AC XY: 9197 AN XY: 74404

Gnomad4 AFR AF: 0.0857

Gnomad4 AMR AF: 0.0939

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.117

Alfa AF: 0.134 Hom.: 2862

Bravo AF: 0.113

Asia WGS AF: 0.136 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12614692; hg19: chr2-240705043;