rs2984920

chr1-192575665-A-Gchr1-192575665-A-T

Variant summary

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

The ENST00000644134.1(ENSG00000285280):n.468-6361T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 1,285,938 control chromosomes in the GnomAD database, including 445,381 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 0.86 (56441 hom., cov: 28)
  • Exomes 𝑓: 0.83 (388940 hom.)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.40

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371664	XR_002958418.2	n.288-8449T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644134.1	n.468-6361T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130256 AN: 151364 Hom.: 56385 Cov.: 28

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.844

GnomAD4 exome AF: 0.827 AC: 938239 AN: 1134460 Hom.: 388940 AF XY: 0.828 AC XY: 461846 AN XY: 557812

Gnomad4 AFR exome AF: 0.960

Gnomad4 AMR exome AF: 0.753

Gnomad4 ASJ exome AF: 0.863

Gnomad4 EAS exome AF: 0.769

Gnomad4 SAS exome AF: 0.896

Gnomad4 FIN exome AF: 0.859

Gnomad4 NFE exome AF: 0.821

Gnomad4 OTH exome AF: 0.839

GnomAD4 genome AF: 0.861 AC: 130367 AN: 151478 Hom.: 56441 Cov.: 28 AF XY: 0.863 AC XY: 63796 AN XY: 73916

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.840

Alfa AF: 0.840 Hom.: 25067

Bravo AF: 0.859

Asia WGS AF: 0.873 AC: 3036 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	16
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2984920; hg19: chr1-192544795;