rs726032

chr2-175792369-G-A

Variant summary

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

The ENST00000692740.1(ENSG00000289349):n.251-40242G>A 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 0.219 in 152,078 control chromosomes in the GnomAD database, including 3,788 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 (3788 hom., cov: 32)
• Consequence: ENST00000692740.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985962	XR_007087312.1	n.150-6593C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692740.1	n.251-40242G>A		intron_variant, non_coding_transcript_variant
	ENST00000685522.1	n.394-40242G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33293 AN: 151960 Hom.: 3782 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.219 AC: 33327 AN: 152078 Hom.: 3788 Cov.: 32 AF XY: 0.224 AC XY: 16633 AN XY: 74330

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.235

Alfa AF: 0.225 Hom.: 5269

Bravo AF: 0.212

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	14
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726032; hg19: chr2-176657097;