rs6962033

chr7-134643618-G-Achr7-134643618-G-C

Variant summary

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

The XR_007060537.1(LOC124901750):n.29222-23670C>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 0.583 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

Genes affected

LOC124901750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901750	XR_007060537.1	n.29222-23670C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.552

Alfa AF: 0.510 Hom.: 41217

Bravo AF: 0.589

Asia WGS AF: 0.763 AC: 2650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.1
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6962033; hg19: chr7-134328370;