ENST00000481773.2:n.238+3938G>A

Variant names:

• chr3-114218488-G-A
• rs9846423
• ENST00000481773.2:n.238+3938G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000481773.2(ENSG00000241490):​n.238+3938G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0298 in 152,246 control chromosomes in the GnomAD database, including 93 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 0.030 (93 hom., cov: 32)
• Consequence: ENSG00000241490 ENST00000481773.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521
• Publications: 2 publications found

Genes affected

ENSG00000241490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0298 (4542/152246) while in subpopulation NFE AF = 0.0474 (3226/67994). AF 95% confidence interval is 0.0461. There are 93 homozygotes in GnomAd4. There are 1956 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 93 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000481773.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000241490	ENST00000481773.2	TSL:3	n.238+3938G>A		intron	N/A
	ENSG00000241490	ENST00000493033.1	TSL:2	n.160+3938G>A		intron	N/A
	ENSG00000241490	ENST00000779676.1		n.341+3938G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4541 AN: 152128 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.00871

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00560

Gnomad FIN AF: 0.0120

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0474

Gnomad OTH AF: 0.0372

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

GnomAD4 genome AF: 0.0298 AC: 4542 AN: 152246 Hom.: 93 Cov.: 32 AF XY: 0.0263 AC XY: 1956 AN XY: 74456

African (AFR) AF: 0.00871 AC: 362 AN: 41556

American (AMR) AF: 0.0355 AC: 543 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00560 AC: 27 AN: 4818

European-Finnish (FIN) AF: 0.0120 AC: 127 AN: 10618

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0474 AC: 3226 AN: 67994

Other (OTH) AF: 0.0369 AC: 78 AN: 2116

Alfa AF: 0.0472 Hom.: 329

Bravo AF: 0.0321

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.2
DANN	Benign	0.34
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs9846423; hg19: chr3-113937335;