rs7567687

Variant names:

• chr2-129276753-C-T
• rs7567687
• XR_007087234.1:n.277-12197C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007087234.1(LOC105373612):​n.277-12197C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 8 publications found

Genes affected

LOC105373612 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.272 AC: 11284 AN: 41502

American (AMR) AF: 0.361 AC: 5511 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2086 AN: 3464

East Asian (EAS) AF: 0.150 AC: 775 AN: 5166

South Asian (SAS) AF: 0.378 AC: 1821 AN: 4820

European-Finnish (FIN) AF: 0.468 AC: 4946 AN: 10564

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36361 AN: 67980

Other (OTH) AF: 0.467 AC: 986 AN: 2110

Alfa AF: 0.489 Hom.: 68226

Bravo AF: 0.408

Asia WGS AF: 0.275 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.64
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs7567687; hg19: chr2-130034326;