rs17232998

chr4-127399728-C-T

Variant summary

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

The ENST00000504050.5(ENSG00000248491):n.368+1998G>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 0.131 in 151,922 control chromosomes in the GnomAD database, including 1,649 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 0.13 (1649 hom., cov: 32)
• Consequence: ENST00000504050.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724210	XR_001741824.3	n.371+1998G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000504050.5	n.368+1998G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000661442.1	n.363+1998G>A		intron_variant, non_coding_transcript_variant
	ENST00000667124.1	n.236+1998G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19889 AN: 151804 Hom.: 1652 Cov.: 32

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.131 AC: 19879 AN: 151922 Hom.: 1649 Cov.: 32 AF XY: 0.127 AC XY: 9470 AN XY: 74292

Gnomad4 AFR AF: 0.0492

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.156

Alfa AF: 0.165 Hom.: 431

Bravo AF: 0.129

Asia WGS AF: 0.0580 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.95
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17232998; hg19: chr4-128320883;