1-41497010-T-G

Variant names:

• chr1-41497010-T-G
• rs747459
• ENST00000727675.1:n.122+10374T>G

Variant summary

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

The ENST00000727675.1(ENSG00000295052):​n.122+10374T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,268 control chromosomes in the GnomAD database, including 47,205 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 0.78 (47205 hom., cov: 35)
• Consequence: ENSG00000295052 ENST00000727675.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 publications found

Genes affected

ENSG00000295052 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 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
ENSG00000295052	ENST00000727675.1	n.122+10374T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119182 AN: 152150 Hom.: 47142 Cov.: 35

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.784 AC: 119305 AN: 152268 Hom.: 47205 Cov.: 35 AF XY: 0.787 AC XY: 58583 AN XY: 74432

African (AFR) AF: 0.849 AC: 35272 AN: 41566

American (AMR) AF: 0.813 AC: 12445 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2250 AN: 3464

East Asian (EAS) AF: 0.967 AC: 5001 AN: 5172

South Asian (SAS) AF: 0.875 AC: 4226 AN: 4828

European-Finnish (FIN) AF: 0.751 AC: 7962 AN: 10606

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49867 AN: 68002

Other (OTH) AF: 0.748 AC: 1582 AN: 2114

Alfa AF: 0.754 Hom.: 113673

Bravo AF: 0.788

Asia WGS AF: 0.894 AC: 3109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.82
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs747459; hg19: chr1-41962681;