rs7539281

Variant names:

• chr1-162038244-G-A
• rs7539281
• ENST00000430905.2:n.222-769G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-162038244-G-A
• chr1-162038244-G-C

Variant summary

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

The ENST00000430905.2(ENSG00000227818):​n.222-769G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,076 control chromosomes in the GnomAD database, including 12,568 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 0.38 (12568 hom., cov: 32)
• Consequence: ENSG00000227818 ENST00000430905.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570
• Publications: 8 publications found

Genes affected

ENSG00000227818 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 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
ENSG00000227818	ENST00000430905.2	n.222-769G>A		intron_variant	Intron 1 of 2	3
ENSG00000227818	ENST00000809863.1	n.228-1099G>A		intron_variant	Intron 1 of 1
ENSG00000227818	ENST00000809864.1	n.180-931G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57012 AN: 151958 Hom.: 12541 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.375 AC: 57088 AN: 152076 Hom.: 12568 Cov.: 32 AF XY: 0.378 AC XY: 28086 AN XY: 74350

African (AFR) AF: 0.596 AC: 24734 AN: 41480

American (AMR) AF: 0.290 AC: 4427 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3468

East Asian (EAS) AF: 0.525 AC: 2713 AN: 5170

South Asian (SAS) AF: 0.489 AC: 2358 AN: 4820

European-Finnish (FIN) AF: 0.297 AC: 3146 AN: 10588

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17460 AN: 67960

Other (OTH) AF: 0.369 AC: 778 AN: 2106

Alfa AF: 0.296 Hom.: 32650

Bravo AF: 0.380

Asia WGS AF: 0.514 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.93
DANN	Benign	0.64
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs7539281; hg19: chr1-162008034;