rs696367

chr3-108036107-C-Gchr3-108036107-C-T

Variant summary

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

The XR_007095995.1(LOC124906265):n.3037G>C 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 0.0764 in 152,156 control chromosomes in the GnomAD database, including 1,226 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 0.076 (1226 hom., cov: 32)
• Consequence: LOC124906265 XR_007095995.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129

Genes affected

LOC124906265 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124906265	XR_007095995.1	n.3037G>C		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651058.1	n.1802+1284G>C		intron_variant, non_coding_transcript_variant
	ENST00000652445.1	n.1416G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0762 AC: 11588 AN: 152038 Hom.: 1219 Cov.: 32

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0819

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

GnomAD4 genome AF: 0.0764 AC: 11618 AN: 152156 Hom.: 1226 Cov.: 32 AF XY: 0.0854 AC XY: 6350 AN XY: 74380

Gnomad4 AFR AF: 0.0814

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0329

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.0602

Gnomad4 NFE AF: 0.0204

Gnomad4 OTH AF: 0.0853

Alfa AF: 0.0121 Hom.: 6

Bravo AF: 0.0824

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	5.3
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs696367; hg19: chr3-107754954;