rs4746077

Variant names:

• chr10-71020361-T-A
• rs4746077
• ENST00000646051.1:n.259-6218T>A

Variant summary

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

The ENST00000646051.1(ENSG00000285300):​n.259-6218T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,208 control chromosomes in the GnomAD database, including 52,887 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 0.83 (52887 hom., cov: 33)
• Consequence: ENSG00000285300 ENST00000646051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 0 publications found

Genes affected

ENSG00000285300 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.859 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
ENSG00000285300	ENST00000646051.1	n.259-6218T>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126520 AN: 152090 Hom.: 52843 Cov.: 33

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.832 AC: 126620 AN: 152208 Hom.: 52887 Cov.: 33 AF XY: 0.829 AC XY: 61678 AN XY: 74406

African (AFR) AF: 0.813 AC: 33726 AN: 41506

American (AMR) AF: 0.748 AC: 11442 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3128 AN: 3472

East Asian (EAS) AF: 0.742 AC: 3833 AN: 5164

South Asian (SAS) AF: 0.799 AC: 3852 AN: 4824

European-Finnish (FIN) AF: 0.846 AC: 8971 AN: 10602

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58845 AN: 68014

Other (OTH) AF: 0.852 AC: 1802 AN: 2116

Alfa AF: 0.845 Hom.: 6742

Bravo AF: 0.824

Asia WGS AF: 0.775 AC: 2694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.5
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4746077; hg19: chr10-72780118;