rs2804923

Positions:

• chr6-13573631-C-T

Variant summary

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

The XR_926497.4(LOC105374937):​n.470+334G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,944 control chromosomes in the GnomAD database, including 26,429 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 0.59 (26429 hom., cov: 31)
• Consequence: LOC105374937 XR_926497.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

Genes affected

LOC105374937 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374937	XR_926497.4	n.470+334G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88933 AN: 151826 Hom.: 26375 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.586 AC: 89047 AN: 151944 Hom.: 26429 Cov.: 31 AF XY: 0.586 AC XY: 43498 AN XY: 74244

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.610

Alfa AF: 0.578 Hom.: 4164

Bravo AF: 0.584

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2804923; hg19: chr6-13573863;