rs309753

Variant names:

• chr4-176453492-C-A
• rs309753
• XR_007058377.1:n.3327C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-176453492-C-A
• chr4-176453492-C-G
• chr4-176453492-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058377.1(LOC124900817):​n.3327C>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_007058377.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746
• Publications: 2 publications found

Genes affected

LOC124900817 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124900817	XR_007058377.1	n.3327C>A		non_coding_transcript_exon_variant	Exon 4 of 4
LOC124900817	XR_007058378.1	n.3207C>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC124900817	XR_007058376.1	n.1157+2668C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.887 AC: 36822 AN: 41490

American (AMR) AF: 0.781 AC: 11931 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3043 AN: 3468

East Asian (EAS) AF: 0.768 AC: 3976 AN: 5180

South Asian (SAS) AF: 0.752 AC: 3626 AN: 4824

European-Finnish (FIN) AF: 0.781 AC: 8278 AN: 10602

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55356 AN: 67988

Other (OTH) AF: 0.809 AC: 1705 AN: 2108

Alfa AF: 0.816 Hom.: 196285

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
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs309753; hg19: chr4-177374643;