2-175812356-A-G

Variant summary

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

The ENST00000692740.1(ENSG00000289349):n.251-20255A>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 0.735 in 152,238 control chromosomes in the GnomAD database, including 41,920 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 0.74 (41920 hom., cov: 33)
• Consequence: ENST00000692740.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985962	XR_007087312.1	n.149+26534T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692740.1	n.251-20255A>G		intron_variant, non_coding_transcript_variant
	ENST00000685522.1	n.394-20255A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111857 AN: 152120 Hom.: 41871 Cov.: 33

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.735 AC: 111963 AN: 152238 Hom.: 41920 Cov.: 33 AF XY: 0.736 AC XY: 54765 AN XY: 74428

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.712

Alfa AF: 0.677 Hom.: 63429

Bravo AF: 0.739

Asia WGS AF: 0.774 AC: 2694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.82
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1446829; hg19: chr2-176677084;