chr6-32718307-G-A

Variant names:

• chr6-32718307-G-A
• rs12177980
• ENST00000585372.2:n.279G>A

Variant summary

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

Score: -12 - Benign

-12

BP4_StrongBA1

The ENST00000585372.2(ENSG00000232080):​n.279G>A 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 0.378 in 152,058 control chromosomes in the GnomAD database, including 12,061 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 0.38 (12061 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000232080 ENST00000585372.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 22 publications found

Genes affected

ENSG00000232080 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102725019	NR_190902.1	n.129+160G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232080	ENST00000585372.2	n.279G>A		non_coding_transcript_exon_variant	Exon 1 of 2	3
ENSG00000232080	ENST00000448198.3	n.145+160G>A		intron_variant	Intron 1 of 1	2
ENSG00000232080	ENST00000621553.1	n.120-99G>A		intron_variant	Intron 1 of 2	5
ENSG00000232080	ENST00000458375.1	n.-78G>A		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57363 AN: 151938 Hom.: 12052 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.369

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.378 AC: 57405 AN: 152058 Hom.: 12061 Cov.: 31 AF XY: 0.386 AC XY: 28691 AN XY: 74322

African (AFR) AF: 0.207 AC: 8599 AN: 41486

American (AMR) AF: 0.437 AC: 6681 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1355 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3193 AN: 5168

South Asian (SAS) AF: 0.486 AC: 2343 AN: 4818

European-Finnish (FIN) AF: 0.538 AC: 5683 AN: 10564

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28004 AN: 67960

Other (OTH) AF: 0.378 AC: 798 AN: 2110

Alfa AF: 0.401 Hom.: 18495

Bravo AF: 0.365

Asia WGS AF: 0.546 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.2
DANN	Benign	0.53
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs12177980; hg19: chr6-32686084;