rs2048741

Variant names:

• chr9-117874984-G-A
• rs2048741
• ENST00000449730.1:n.127C>T

Variant summary

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

The ENST00000449730.1(ENSG00000231901):​n.127C>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 0.419 in 152,030 control chromosomes in the GnomAD database, including 13,436 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 0.42 (13436 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000231901 ENST00000449730.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 4 publications found

Genes affected

ENSG00000231901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376243	XR_001746917.3	n.3581C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231901	ENST00000449730.1	n.127C>T		non_coding_transcript_exon_variant	Exon 2 of 4	3
ENSG00000284977	ENST00000644180.1	n.5294G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000285082	ENST00000646089.2	c.*17-1831G>A		intron_variant	Intron 2 of 2			ENSP00000496197.1

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63693 AN: 151908 Hom.: 13420 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.437

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.419 AC: 63745 AN: 152028 Hom.: 13436 Cov.: 32 AF XY: 0.419 AC XY: 31132 AN XY: 74312

African (AFR) AF: 0.410 AC: 17008 AN: 41484

American (AMR) AF: 0.496 AC: 7566 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1611 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1588 AN: 5172

South Asian (SAS) AF: 0.306 AC: 1476 AN: 4816

European-Finnish (FIN) AF: 0.393 AC: 4146 AN: 10558

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28938 AN: 67960

Other (OTH) AF: 0.439 AC: 929 AN: 2114

Alfa AF: 0.425 Hom.: 44337

Bravo AF: 0.427

Asia WGS AF: 0.302 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.66
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2048741; hg19: chr9-120637262;