chr2-129276753-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373612	XR_007087234.1	n.277-12197C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

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 v4.3

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;