rs72734930

Variant names:

• chr1-192543429-G-A
• rs72734930
• ENST00000434300.2:n.182+23718C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-192543429-G-A
• chr1-192543429-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000434300.2(ENSG00000285280):​n.182+23718C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 152,172 control chromosomes in the GnomAD database, including 50 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 0.019 (50 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000434300.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

Genes affected

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

LOC105371664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0188 (2864/152172) while in subpopulation AMR AF= 0.0272 (415/15284). AF 95% confidence interval is 0.025. There are 50 homozygotes in gnomad4. There are 1338 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 50 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.357+23718C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000434300.2	n.182+23718C>T		intron_variant	Intron 3 of 3	5
ENSG00000285280	ENST00000642855.1	n.409+23718C>T		intron_variant	Intron 4 of 7
ENSG00000285280	ENST00000644058.1	n.626+23718C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0188 AC: 2866 AN: 152056 Hom.: 50 Cov.: 32

Gnomad AFR AF: 0.00432

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0586

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0178

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

GnomAD4 genome AF: 0.0188 AC: 2864 AN: 152172 Hom.: 50 Cov.: 32 AF XY: 0.0180 AC XY: 1338 AN XY: 74392

Gnomad4 AFR AF: 0.00431

Gnomad4 AMR AF: 0.0272

Gnomad4 ASJ AF: 0.0586

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0113

Gnomad4 NFE AF: 0.0248

Gnomad4 OTH AF: 0.0176

Alfa AF: 0.00987 Hom.: 2

Bravo AF: 0.0194

Asia WGS AF: 0.00837 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72734930; hg19: chr1-192512559;