rs493950

Variant names:

• chr1-228419264-A-G
• rs493950
• ENST00000701501.2:n.304-8899A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-228419264-A-G
• chr1-228419264-A-T

Variant summary

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

The ENST00000701501.2(ENSG00000231563):​n.304-8899A>G variant causes a intron 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: ENSG00000231563 ENST00000701501.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 4 publications found

Genes affected

ENSG00000231563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231563	ENST00000701501.2	n.304-8899A>G		intron_variant	Intron 1 of 1
ENSG00000231563	ENST00000730655.1	n.302+11786A>G		intron_variant	Intron 1 of 1
ENSG00000231563	ENST00000730656.1	n.254+11786A>G		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.685 AC: 28385 AN: 41428

American (AMR) AF: 0.183 AC: 2791 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3468

East Asian (EAS) AF: 0.403 AC: 2086 AN: 5176

South Asian (SAS) AF: 0.164 AC: 790 AN: 4824

European-Finnish (FIN) AF: 0.198 AC: 2090 AN: 10576

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7302 AN: 67996

Other (OTH) AF: 0.240 AC: 505 AN: 2108

Alfa AF: 0.155 Hom.: 5652

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs493950; hg19: chr1-228606965;