chr2-157049696-A-G

Position:

• chr2-157049696-A-G

Variant summary

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

The ENST00000653962.1(ENSG00000286530):​n.1007A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,192 control chromosomes in the GnomAD database, including 57,069 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 0.86 (57069 hom., cov: 32)
• Consequence: ENSG00000286530 ENST00000653962.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

Genes affected

ENSG00000286530 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373709	XR_001739755.2	n.1912A>G		non_coding_transcript_exon_variant	4/4
LOC105373709	XR_923507.3	n.1571A>G		non_coding_transcript_exon_variant	5/5
LOC105373710	XR_923509.3	n.70+6492T>C		intron_variant
LOC105373710	XR_923510.3	n.70+6492T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286530	ENST00000653962.1	n.1007A>G		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131098 AN: 152074 Hom.: 57021 Cov.: 32

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.862 AC: 131201 AN: 152192 Hom.: 57069 Cov.: 32 AF XY: 0.863 AC XY: 64192 AN XY: 74400

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.845

Alfa AF: 0.826 Hom.: 48931

Bravo AF: 0.867

Asia WGS AF: 0.766 AC: 2665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.94
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: rs1481385; hg19: chr2-157906208;