rs1933695

chr1-192795690-G-A

Variant summary

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

The ENST00000644134.1(ENSG00000285280):n.105-29496C>T 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 0.119 in 151,990 control chromosomes in the GnomAD database, including 1,400 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 0.12 (1400 hom., cov: 31)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 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
	ENST00000644134.1	n.105-29496C>T		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.194-29496C>T		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.200-3222C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18159 AN: 151872 Hom.: 1399 Cov.: 31

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0472

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.0938

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.119 AC: 18156 AN: 151990 Hom.: 1400 Cov.: 31 AF XY: 0.114 AC XY: 8499 AN XY: 74278

Gnomad4 AFR AF: 0.0385

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0473

Gnomad4 SAS AF: 0.0624

Gnomad4 FIN AF: 0.0938

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.142

Alfa AF: 0.166 Hom.: 3069

Bravo AF: 0.120

Asia WGS AF: 0.0660 AC: 232 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	2.5
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: rs1933695; hg19: chr1-192764820;