XR_007060537.1:n.29222-24259G>C

Variant names:

• chr7-134644207-C-G
• rs3757397
• XR_007060537.1:n.29222-24259G>C

Variant summary

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

The XR_007060537.1(LOC124901750):​n.29222-24259G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,962 control chromosomes in the GnomAD database, including 26,829 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 0.58 (26829 hom., cov: 31)
• Consequence: LOC124901750 XR_007060537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• Publications: 2 publications found

Genes affected

LOC124901750 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88509 AN: 151844 Hom.: 26805 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.583 AC: 88591 AN: 151962 Hom.: 26829 Cov.: 31 AF XY: 0.589 AC XY: 43764 AN XY: 74260

African (AFR) AF: 0.711 AC: 29479 AN: 41474

American (AMR) AF: 0.563 AC: 8591 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1758 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4579 AN: 5154

South Asian (SAS) AF: 0.717 AC: 3454 AN: 4816

European-Finnish (FIN) AF: 0.532 AC: 5593 AN: 10520

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33353 AN: 67948

Other (OTH) AF: 0.553 AC: 1165 AN: 2108

Alfa AF: 0.524 Hom.: 2692

Bravo AF: 0.589

Asia WGS AF: 0.763 AC: 2650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.38
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs3757397; hg19: chr7-134328959;