6-80530312-T-G

Variant names:

• chr6-80530312-T-G
• rs484019
• XR_942720.3:n.587A>C

Variant summary

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

The XR_942720.3(LOC105377869):​n.587A>C 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 0.501 in 151,936 control chromosomes in the GnomAD database, including 19,612 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 0.50 (19612 hom., cov: 33)
• Consequence: LOC105377869 XR_942720.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• Publications: 4 publications found

Genes affected

LOC105377869 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377869	XR_942720.3	n.587A>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC112267962	XR_002956360.2	n.90+45247T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299370	ENST00000762913.1	n.*139A>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76023 AN: 151816 Hom.: 19602 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.501 AC: 76066 AN: 151936 Hom.: 19612 Cov.: 33 AF XY: 0.503 AC XY: 37357 AN XY: 74272

African (AFR) AF: 0.379 AC: 15725 AN: 41478

American (AMR) AF: 0.573 AC: 8729 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2204 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3434 AN: 5146

South Asian (SAS) AF: 0.709 AC: 3417 AN: 4818

European-Finnish (FIN) AF: 0.458 AC: 4843 AN: 10580

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35986 AN: 67894

Other (OTH) AF: 0.540 AC: 1140 AN: 2112

Alfa AF: 0.525 Hom.: 20655

Bravo AF: 0.502

Asia WGS AF: 0.672 AC: 2338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.63
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs484019; hg19: chr6-81240029; COSMIC: COSV69407604;