19-49720009-G-A

Variant names:

• chr19-49720009-G-A
• rs3810265
• ENST00000498085.1:n.73C>T

Variant summary

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

The ENST00000498085.1(ENSG00000243829):​n.73C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 1,611,544 control chromosomes in the GnomAD database, including 2,625 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 0.060 (677 hom., cov: 31)
  • Exomes 𝑓: 0.017 (1948 hom.)
• Consequence: ENSG00000243829 ENST00000498085.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77
• Publications: 8 publications found

Genes affected

ENSG00000243829 (HGNC:):

RPS9P4 (HGNC:36710):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498085.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243829	ENST00000498085.1	TSL:6	n.73C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000295494	ENST00000730480.1		n.695+74G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9048 AN: 151904 Hom.: 673 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.00312

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00176

Gnomad OTH AF: 0.0527

GnomAD4 exome AF: 0.0169 AC: 24627 AN: 1459524 Hom.: 1948 Cov.: 33 AF XY: 0.0158 AC XY: 11494 AN XY: 726084

African (AFR) AF: 0.157 AC: 5254 AN: 33388

American (AMR) AF: 0.174 AC: 7768 AN: 44694

Ashkenazi Jewish (ASJ) AF: 0.00394 AC: 103 AN: 26128

East Asian (EAS) AF: 0.178 AC: 7047 AN: 39696

South Asian (SAS) AF: 0.0194 AC: 1673 AN: 86156

European-Finnish (FIN) AF: 0.00307 AC: 164 AN: 53414

Middle Eastern (MID) AF: 0.0109 AC: 45 AN: 4136

European-Non Finnish (NFE) AF: 0.000980 AC: 1090 AN: 1111718

Other (OTH) AF: 0.0246 AC: 1483 AN: 60194

GnomAD4 genome AF: 0.0597 AC: 9069 AN: 152020 Hom.: 677 Cov.: 31 AF XY: 0.0599 AC XY: 4451 AN XY: 74310

African (AFR) AF: 0.149 AC: 6164 AN: 41448

American (AMR) AF: 0.110 AC: 1681 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.00432 AC: 15 AN: 3472

East Asian (EAS) AF: 0.159 AC: 819 AN: 5148

South Asian (SAS) AF: 0.0256 AC: 123 AN: 4814

European-Finnish (FIN) AF: 0.00312 AC: 33 AN: 10584

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00176 AC: 120 AN: 67992

Other (OTH) AF: 0.0521 AC: 110 AN: 2110

Alfa AF: 0.0269 Hom.: 45

Bravo AF: 0.0749

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	8.3
DANN	Benign	0.97
PhyloP100		1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3810265;

hg19: chr19-50223266;