rs853803

Positions:

• chr5-68466276-A-G
• chr5-68466276-A-T

Variant summary

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

The XR_007058804.1(LOC105379013):​n.474-32691T>C 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 0.304 in 151,990 control chromosomes in the GnomAD database, including 7,410 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 0.30 (7410 hom., cov: 32)
• Consequence: LOC105379013 XR_007058804.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985

Genes affected

LOC105379013 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379013	XR_007058804.1	n.474-32691T>C		intron_variant, non_coding_transcript_variant
LOC105379013	XR_007058805.1	n.144-32691T>C		intron_variant, non_coding_transcript_variant
LOC105379013	XR_007058806.1	n.2260-32691T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46087 AN: 151872 Hom.: 7389 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.304 AC: 46143 AN: 151990 Hom.: 7410 Cov.: 32 AF XY: 0.309 AC XY: 22926 AN XY: 74284

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.316

Alfa AF: 0.289 Hom.: 13904

Bravo AF: 0.321

Asia WGS AF: 0.421 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.48
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs853803; hg19: chr5-67762103;