rs10488432

Positions:

• chr7-134623673-T-C

Variant summary

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

The XR_007060537.1(LOC124901750):​n.29222-3725A>G 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 0.128 in 152,174 control chromosomes in the GnomAD database, including 1,417 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 0.13 (1417 hom., cov: 32)
• Consequence: LOC124901750 XR_007060537.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

LOC124901750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901750	XR_007060537.1	n.29222-3725A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19492 AN: 152056 Hom.: 1412 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.128 AC: 19508 AN: 152174 Hom.: 1417 Cov.: 32 AF XY: 0.130 AC XY: 9695 AN XY: 74394

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0679

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.137

Alfa AF: 0.130 Hom.: 139

Bravo AF: 0.130

Asia WGS AF: 0.122 AC: 426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488432; hg19: chr7-134308425;