1-11908021-C-G

Position:

• chr1-11908021-C-G

Variant summary

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

The ENST00000661075.1(ENSG00000285646):​n.82C>G 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 0.353 in 152,080 control chromosomes in the GnomAD database, including 9,873 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 0.35 (9873 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000285646 ENST00000661075.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

Genes affected

ENSG00000285646 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285646	ENST00000661075.1	n.82C>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53563 AN: 151960 Hom.: 9857 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.346

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.353 AC: 53618 AN: 152078 Hom.: 9873 Cov.: 33 AF XY: 0.360 AC XY: 26736 AN XY: 74340

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.347

Alfa AF: 0.238 Hom.: 667

Bravo AF: 0.337

Asia WGS AF: 0.444 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	3.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6671723; hg19: chr1-11968078;