chr6-80530312-T-G

Position:

• chr6-80530312-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105377869 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105377869	XR_942720.3	n.587A>C		non_coding_transcript_exon_variant	3/3
		n.80530312T>G		intergenic_region
LOC112267962	XR_002956360.2	n.90+45247T>G		intron_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.540

Alfa AF: 0.524 Hom.: 12485

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

Splicing

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

Publications

LitVar

Other links and lift over

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