rs7567687

Positions:

• chr2-129276753-C-T

Variant summary

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

The XR_007087234.1(LOC105373612):​n.277-12197C>T 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 0.424 in 152,096 control chromosomes in the GnomAD database, including 14,894 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 0.42 (14894 hom., cov: 33)
• Consequence: LOC105373612 XR_007087234.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

Genes affected

LOC105373612 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373612	XR_007087234.1	n.277-12197C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64482 AN: 151976 Hom.: 14889 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.424 AC: 64503 AN: 152096 Hom.: 14894 Cov.: 33 AF XY: 0.419 AC XY: 31174 AN XY: 74330

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.467

Alfa AF: 0.506 Hom.: 46682

Bravo AF: 0.408

Asia WGS AF: 0.275 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7567687; hg19: chr2-130034326;