rs1024461

Variant names:

• chr4-104741614-C-T
• rs1024461
• ENST00000515127.1:n.407+5026G>A

Variant summary

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

The ENST00000515127.1(ENSG00000248242):​n.407+5026G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,132 control chromosomes in the GnomAD database, including 1,961 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 (1961 hom., cov: 32)
• Consequence: ENSG00000248242 ENST00000515127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 2 publications found

Genes affected

ENSG00000248242 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248242	ENST00000515127.1	n.407+5026G>A		intron_variant	Intron 4 of 5	5
ENSG00000248242	ENST00000723032.1	n.333+5026G>A		intron_variant	Intron 2 of 5
ENSG00000248242	ENST00000723033.1	n.612+5026G>A		intron_variant	Intron 3 of 4
ENSG00000248242	ENST00000723034.1	n.431+5026G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21870 AN: 152014 Hom.: 1951 Cov.: 32

Gnomad AFR AF: 0.0363

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.144 AC: 21891 AN: 152132 Hom.: 1961 Cov.: 32 AF XY: 0.144 AC XY: 10700 AN XY: 74376

African (AFR) AF: 0.0362 AC: 1503 AN: 41520

American (AMR) AF: 0.217 AC: 3316 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 490 AN: 3470

East Asian (EAS) AF: 0.142 AC: 737 AN: 5172

South Asian (SAS) AF: 0.232 AC: 1115 AN: 4814

European-Finnish (FIN) AF: 0.118 AC: 1246 AN: 10582

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12958 AN: 67978

Other (OTH) AF: 0.154 AC: 325 AN: 2116

Alfa AF: 0.159 Hom.: 286

Bravo AF: 0.148

Asia WGS AF: 0.163 AC: 565 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.33
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1024461; hg19: chr4-105662771;