rs7661032

chr4-132985377-T-G

Variant summary

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

The XR_007058479.1(LOC124900861):n.150+135A>C 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 0.0333 in 152,206 control chromosomes in the GnomAD database, including 195 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 0.033 (195 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LOC124900861 XR_007058479.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

Genes affected

LOC124900861 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900861	XR_007058479.1	n.150+135A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0332 AC: 5048 AN: 152088 Hom.: 195 Cov.: 32

Gnomad AFR AF: 0.0954

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.0265

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00695

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0333 AC: 5063 AN: 152206 Hom.: 195 Cov.: 32 AF XY: 0.0315 AC XY: 2342 AN XY: 74420

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.0168

Gnomad4 ASJ AF: 0.0254

Gnomad4 EAS AF: 0.0266

Gnomad4 SAS AF: 0.00994

Gnomad4 FIN AF: 0.00188

Gnomad4 NFE AF: 0.00696

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0226 Hom.: 20

Bravo AF: 0.0376

Asia WGS AF: 0.0420 AC: 147 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	1.4
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7661032; hg19: chr4-133906532;