rs3767489

Positions:

• chr1-192746685-C-T

Variant summary

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

The ENST00000644134.1(ENSG00000285280):​n.408+18123G>A 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 0.394 in 152,060 control chromosomes in the GnomAD database, including 12,867 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 0.39 (12867 hom., cov: 32)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 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
	ENST00000644134.1	n.408+18123G>A		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.497+18123G>A		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.673+18123G>A		intron_variant, non_coding_transcript_variant
	ENST00000646999.1	n.564+8236G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59944 AN: 151942 Hom.: 12864 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.430

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.394 AC: 59942 AN: 152060 Hom.: 12867 Cov.: 32 AF XY: 0.394 AC XY: 29271 AN XY: 74306

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.431

Alfa AF: 0.413 Hom.: 2389

Bravo AF: 0.383

Asia WGS AF: 0.500 AC: 1736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
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: rs3767489; hg19: chr1-192715815;