rs1342809

Positions:

• chr1-192801422-G-T

Variant summary

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

The ENST00000644134.1(ENSG00000285280):​n.105-35228C>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 0.118 in 152,118 control chromosomes in the GnomAD database, including 1,387 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 (1387 hom., cov: 33)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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.105-35228C>A		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.194-35228C>A		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.200-8954C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17905 AN: 152000 Hom.: 1386 Cov.: 33

Gnomad AFR AF: 0.0323

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0512

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.118 AC: 17900 AN: 152118 Hom.: 1387 Cov.: 33 AF XY: 0.113 AC XY: 8386 AN XY: 74372

Gnomad4 AFR AF: 0.0322

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0513

Gnomad4 SAS AF: 0.0610

Gnomad4 FIN AF: 0.0940

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.139

Alfa AF: 0.126 Hom.: 209

Bravo AF: 0.118

Asia WGS AF: 0.0650 AC: 229 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342809; hg19: chr1-192770552;