rs309753

chr4-176453492-C-Achr4-176453492-C-Gchr4-176453492-C-T

Variant summary

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

The XR_007058378.1(LOC124900817):n.3207C>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 0.827 in 152,152 control chromosomes in the GnomAD database, including 52,157 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 0.83 (52157 hom., cov: 31)
• Consequence: LOC124900817 XR_007058378.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

Genes affected

LOC124900817 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900817	XR_007058378.1	n.3207C>A		non_coding_transcript_exon_variant	3/3
LOC124900817	XR_007058377.1	n.3327C>A		non_coding_transcript_exon_variant	4/4
LOC124900817	XR_007058376.1	n.1157+2668C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125702 AN: 152034 Hom.: 52111 Cov.: 31

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.827 AC: 125806 AN: 152152 Hom.: 52157 Cov.: 31 AF XY: 0.823 AC XY: 61225 AN XY: 74396

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.809

Alfa AF: 0.813 Hom.: 84209

Bravo AF: 0.829

Asia WGS AF: 0.751 AC: 2611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.64
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs309753; hg19: chr4-177374643;