rs726033

Positions:

• chr2-175792525-C-A
• chr2-175792525-C-T

Variant summary

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

The ENST00000685522.1(ENSG00000289349):​n.394-40086C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,130 control chromosomes in the GnomAD database, including 7,181 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 0.30 (7181 hom., cov: 33)
• Consequence: ENSG00000289349 ENST00000685522.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

Genes affected

ENSG00000289349 (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 (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985962	XR_007087312.1	n.150-6749G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289349	ENST00000685522.1	n.394-40086C>A		intron_variant
ENSG00000289349	ENST00000692740.1	n.251-40086C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45442 AN: 152012 Hom.: 7163 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.299 AC: 45515 AN: 152130 Hom.: 7181 Cov.: 33 AF XY: 0.301 AC XY: 22392 AN XY: 74364

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.307

Alfa AF: 0.171 Hom.: 356

Bravo AF: 0.299

Asia WGS AF: 0.330 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726033; hg19: chr2-176657253;