rs1024461

Positions:

• chr4-104741614-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000515127.1(ENSG00000248242):​n.407+5026G>A variant causes a intron, non coding transcript 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: ENST00000515127.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000515127.1	n.407+5026G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0362

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.154

Alfa AF: 0.163 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1024461; hg19: chr4-105662771;