rs4734457

Positions:

• chr8-100492129-C-A

Variant summary

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

The XR_007061031.1(LOC124901992):​n.12568C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,134 control chromosomes in the GnomAD database, including 1,639 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 (1639 hom., cov: 32)
• Consequence: LOC124901992 XR_007061031.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.772

Genes affected

LOC124901992 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901992	XR_007061031.1	n.12568C>A		non_coding_transcript_exon_variant	1/2
LOC124901992	XR_007061032.1	n.12568C>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665530.1	n.168-8032C>A		intron_variant, non_coding_transcript_variant
	ENST00000523831.1	n.148-8836C>A		intron_variant, non_coding_transcript_variant		2
	ENST00000689055.1	n.165-8032C>A		intron_variant, non_coding_transcript_variant
	ENST00000701278.1	n.165-8633C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20372 AN: 152016 Hom.: 1634 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.134 AC: 20396 AN: 152134 Hom.: 1639 Cov.: 32 AF XY: 0.135 AC XY: 10070 AN XY: 74376

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.0444

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.139

Alfa AF: 0.117 Hom.: 1183

Bravo AF: 0.148

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4734457; hg19: chr8-101504357;