2-110691564-A-G

Variant summary

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

The ENST00000703531.1(ENSG00000289202):n.373+12967A>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 0.838 in 152,208 control chromosomes in the GnomAD database, including 53,797 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 0.84 (53797 hom., cov: 32)
• Consequence: ENST00000703531.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373554	XR_007087178.1	n.3799-955A>G		intron_variant, non_coding_transcript_variant
LOC105373554	XR_923189.4	n.387-955A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000703531.1	n.373+12967A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127394 AN: 152090 Hom.: 53743 Cov.: 32

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.838 AC: 127510 AN: 152208 Hom.: 53797 Cov.: 32 AF XY: 0.838 AC XY: 62358 AN XY: 74382

Gnomad4 AFR AF: 0.947

Gnomad4 AMR AF: 0.873

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.805

Alfa AF: 0.795 Hom.: 40866

Bravo AF: 0.846

Asia WGS AF: 0.764 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.0
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11694702; hg19: chr2-111449141;