rs16834456

Variant names:

• chr1-192581407-C-A
• rs16834456
• ENST00000434300.3:n.164+12192G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434300.3(ENSG00000285280):​n.164+12192G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,030 control chromosomes in the GnomAD database, including 2,847 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 0.15 (2847 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000434300.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 7 publications found

Genes affected

ENSG00000285280 (HGNC:49018): (RSG2 antisense RNA 1)

LOC105371664 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.287+12192G>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000434300.3	n.164+12192G>T		intron_variant	Intron 2 of 3	5
ENSG00000285280	ENST00000642855.1	n.339+12192G>T		intron_variant	Intron 3 of 7
ENSG00000285280	ENST00000644058.2	n.564+12192G>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22957 AN: 151912 Hom.: 2842 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.0479

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0844

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.151 AC: 22987 AN: 152030 Hom.: 2847 Cov.: 32 AF XY: 0.147 AC XY: 10948 AN XY: 74304

African (AFR) AF: 0.344 AC: 14238 AN: 41420

American (AMR) AF: 0.0861 AC: 1314 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0479 AC: 166 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0758 AC: 366 AN: 4826

European-Finnish (FIN) AF: 0.0802 AC: 850 AN: 10600

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0844 AC: 5735 AN: 67974

Other (OTH) AF: 0.111 AC: 233 AN: 2104

Alfa AF: 0.127 Hom.: 267

Bravo AF: 0.161

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.75
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs16834456; hg19: chr1-192550537;