1-5304574-C-T

Variant names:

• chr1-5304574-C-T
• rs9439519
• ENST00000641871.1:n.909G>A

Variant summary

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

The ENST00000641871.1(ENSG00000284616):​n.909G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,982 control chromosomes in the GnomAD database, including 29,845 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 0.62 (29844 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: ENSG00000284616 ENST00000641871.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 9 publications found

Genes affected

ENSG00000284616 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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
ENSG00000284616	ENST00000641871.1	n.909G>A		non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94764 AN: 151860 Hom.: 29801 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.612

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.500 AC: 1 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.624 AC: 94861 AN: 151978 Hom.: 29844 Cov.: 32 AF XY: 0.628 AC XY: 46662 AN XY: 74266

African (AFR) AF: 0.691 AC: 28638 AN: 41456

American (AMR) AF: 0.560 AC: 8549 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2194 AN: 3470

East Asian (EAS) AF: 0.700 AC: 3617 AN: 5166

South Asian (SAS) AF: 0.613 AC: 2951 AN: 4814

European-Finnish (FIN) AF: 0.667 AC: 7023 AN: 10534

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39979 AN: 67950

Other (OTH) AF: 0.614 AC: 1293 AN: 2106

Alfa AF: 0.602 Hom.: 6371

Bravo AF: 0.618

Asia WGS AF: 0.673 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.51
DANN	Benign	0.20
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9439519; hg19: chr1-5364634;