rs2994906

Positions:

• chr13-25118954-A-G

Variant summary

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

The XR_007063728.1(LOC105370120):​n.335A>G 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 0.798 in 151,774 control chromosomes in the GnomAD database, including 48,431 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 0.80 (48431 hom., cov: 28)
• Consequence: LOC105370120 XR_007063728.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

LOC105370120 (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 (SAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370120	XR_007063728.1	n.335A>G		non_coding_transcript_exon_variant	3/3
LOC105370120	XR_007063725.1	n.618A>G		non_coding_transcript_exon_variant	2/2
LOC105370120	XR_007063726.1	n.341A>G		non_coding_transcript_exon_variant	3/3
LOC105370120	XR_007063727.1	n.1220A>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121091 AN: 151656 Hom.: 48400 Cov.: 28

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.798 AC: 121177 AN: 151774 Hom.: 48431 Cov.: 28 AF XY: 0.801 AC XY: 59474 AN XY: 74204

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.810

Alfa AF: 0.787 Hom.: 11703

Bravo AF: 0.806

Asia WGS AF: 0.833 AC: 2897 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	0.0030
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2994906; hg19: chr13-25693092;