chr1-192585301-G-T

Variant names:

• chr1-192585301-G-T
• rs6428106
• ENST00000434300.3:n.164+8298C>A

Variant summary

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

The ENST00000434300.3(ENSG00000285280):​n.164+8298C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 151,914 control chromosomes in the GnomAD database, including 1,605 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 0.14 (1605 hom., cov: 31)
• Consequence: ENSG00000285280 ENST00000434300.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.287+8298C>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000434300.3	n.164+8298C>A		intron_variant	Intron 2 of 3	5
ENSG00000285280	ENST00000642855.1	n.339+8298C>A		intron_variant	Intron 3 of 7
ENSG00000285280	ENST00000644058.2	n.564+8298C>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21261 AN: 151796 Hom.: 1603 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.140 AC: 21275 AN: 151914 Hom.: 1605 Cov.: 31 AF XY: 0.144 AC XY: 10696 AN XY: 74254

African (AFR) AF: 0.190 AC: 7860 AN: 41388

American (AMR) AF: 0.107 AC: 1625 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3468

East Asian (EAS) AF: 0.0777 AC: 402 AN: 5172

South Asian (SAS) AF: 0.227 AC: 1091 AN: 4816

European-Finnish (FIN) AF: 0.173 AC: 1823 AN: 10558

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7703 AN: 67944

Other (OTH) AF: 0.113 AC: 237 AN: 2106

Alfa AF: 0.133 Hom.: 175

Bravo AF: 0.133

Asia WGS AF: 0.160 AC: 556 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.27
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6428106; hg19: chr1-192554431;