7-134643618-G-A

Variant names:

• chr7-134643618-G-A
• rs6962033
• XR_007060537.1:n.29222-23670C>T

Variant summary

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

The XR_007060537.1(LOC124901750):​n.29222-23670C>T 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 152,102 control chromosomes in the GnomAD database, including 26,893 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 (26893 hom., cov: 33)
• Consequence: LOC124901750 XR_007060537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88642 AN: 151982 Hom.: 26868 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.583 AC: 88726 AN: 152102 Hom.: 26893 Cov.: 33 AF XY: 0.590 AC XY: 43865 AN XY: 74350

African (AFR) AF: 0.711 AC: 29517 AN: 41490

American (AMR) AF: 0.563 AC: 8601 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1756 AN: 3470

East Asian (EAS) AF: 0.889 AC: 4603 AN: 5178

South Asian (SAS) AF: 0.718 AC: 3461 AN: 4822

European-Finnish (FIN) AF: 0.534 AC: 5634 AN: 10556

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

European-Non Finnish (NFE) AF: 0.491 AC: 33370 AN: 67986

Other (OTH) AF: 0.552 AC: 1164 AN: 2108

Alfa AF: 0.521 Hom.: 90499

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	-0.91
CADD	Benign	2.1
DANN	Benign	0.39
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs6962033; hg19: chr7-134328370;