rs12664788

Positions:

• chr6-82264372-G-T

Variant summary

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

The ENST00000401636.1(ENSG00000220537):​n.603C>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 0.1 in 441,436 control chromosomes in the GnomAD database, including 3,260 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 0.13 (1792 hom., cov: 32)
  • Exomes 𝑓: 0.086 (1468 hom.)
• Consequence: ENST00000401636.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000401636.1	n.603C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19521 AN: 152018 Hom.: 1795 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0730

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.0965

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.0856 AC: 24770 AN: 289300 Hom.: 1468 Cov.: 0 AF XY: 0.0849 AC XY: 13818 AN XY: 162722

Gnomad4 AFR exome AF: 0.246

Gnomad4 AMR exome AF: 0.113

Gnomad4 ASJ exome AF: 0.0718

Gnomad4 EAS exome AF: 0.186

Gnomad4 SAS exome AF: 0.0956

Gnomad4 FIN exome AF: 0.111

Gnomad4 NFE exome AF: 0.0561

Gnomad4 OTH exome AF: 0.0856

GnomAD4 genome AF: 0.128 AC: 19533 AN: 152136 Hom.: 1792 Cov.: 32 AF XY: 0.132 AC XY: 9822 AN XY: 74380

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0730

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.0966

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0567

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0767 Hom.: 1100

Bravo AF: 0.134

Asia WGS AF: 0.147 AC: 510 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	4.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12664788; hg19: chr6-82974089;