rs493950

chr1-228419264-A-Gchr1-228419264-A-T

Variant summary

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

The ENST00000701501.1(ENSG00000231563):n.284-8899A>G 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 0.293 in 152,058 control chromosomes in the GnomAD database, including 11,267 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 0.29 (11267 hom., cov: 32)
• Consequence: ENST00000701501.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701501.1	n.284-8899A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44530 AN: 151940 Hom.: 11237 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.293 AC: 44609 AN: 152058 Hom.: 11267 Cov.: 32 AF XY: 0.294 AC XY: 21876 AN XY: 74340

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.240

Alfa AF: 0.138 Hom.: 3286

Bravo AF: 0.313

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.6
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs493950; hg19: chr1-228606965;