rs3795617

Positions:

• chr1-192634560-C-T

Variant summary

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

The variant allele was found at a frequency of 0.438 in 151,790 control chromosomes in the GnomAD database, including 14,820 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 0.44 (14820 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.192634560C>T		intergenic_region
LOC107985241	XR_001738348.2	n.*10C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000434300.2	n.54-40903G>A		intron_variant		5
ENSG00000285280	ENST00000644058.1	n.498-40903G>A		intron_variant
ENSG00000285280	ENST00000644134.1	n.409-40903G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66458 AN: 151672 Hom.: 14807 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.438 AC: 66509 AN: 151790 Hom.: 14820 Cov.: 32 AF XY: 0.438 AC XY: 32494 AN XY: 74172

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.426

Alfa AF: 0.465 Hom.: 8030

Bravo AF: 0.429

Asia WGS AF: 0.358 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3795617; hg19: chr1-192603690; COSMIC: COSV67345786;