rs1583971

Variant names:

• chr4-99485865-T-A
• rs1583971
• ENST00000506494.1:n.103-8978A>T

Variant summary

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

The ENST00000506494.1(ENSG00000250300):​n.103-8978A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,116 control chromosomes in the GnomAD database, including 7,360 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 0.25 (7360 hom., cov: 32)
• Consequence: ENSG00000250300 ENST00000506494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673

Genes affected

ENSG00000250300 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 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
ENSG00000250300	ENST00000506494.1	n.103-8978A>T		intron_variant	Intron 1 of 3	6

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37432 AN: 151998 Hom.: 7322 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.247 AC: 37520 AN: 152116 Hom.: 7360 Cov.: 32 AF XY: 0.249 AC XY: 18512 AN XY: 74388

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.0611

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.225

Alfa AF: 0.182 Hom.: 558

Bravo AF: 0.267

Asia WGS AF: 0.347 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1583971; hg19: chr4-100407022;