rs798601

Positions:

• chr3-118794076-T-A

Variant summary

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

The NR_135547.1(LOC105374060):​n.127+16631A>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 0.331 in 151,844 control chromosomes in the GnomAD database, including 8,463 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 0.33 (8463 hom., cov: 32)
• Consequence: LOC105374060 NR_135547.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

Genes affected

LOC105374060 (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 (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374060	NR_135547.1	n.127+16631A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656350.1	n.130+16631A>T		intron_variant, non_coding_transcript_variant
	ENST00000657445.1	n.51+16631A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50278 AN: 151726 Hom.: 8448 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.331 AC: 50319 AN: 151844 Hom.: 8463 Cov.: 32 AF XY: 0.331 AC XY: 24584 AN XY: 74208

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.325

Alfa AF: 0.339 Hom.: 1130

Bravo AF: 0.326

Asia WGS AF: 0.359 AC: 1247 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	0.13
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs798601; hg19: chr3-118512923;