5-143266338-T-C

Variant names:

• chr5-143266338-T-C
• rs244465
• ENST00000770709.1:n.117+7045T>C

Variant summary

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

The ENST00000770709.1(ENSG00000300303):​n.117+7045T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 151,826 control chromosomes in the GnomAD database, including 59,618 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 0.88 (59618 hom., cov: 29)
• Consequence: ENSG00000300303 ENST00000770709.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 5 publications found

Genes affected

ENSG00000300303 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 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
ENSG00000300303	ENST00000770709.1	n.117+7045T>C		intron_variant	Intron 1 of 3
ENSG00000300303	ENST00000770710.1	n.117+7045T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134030 AN: 151708 Hom.: 59586 Cov.: 29

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.883 AC: 134111 AN: 151826 Hom.: 59618 Cov.: 29 AF XY: 0.881 AC XY: 65382 AN XY: 74226

African (AFR) AF: 0.814 AC: 33683 AN: 41358

American (AMR) AF: 0.811 AC: 12365 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3337 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3817 AN: 5170

South Asian (SAS) AF: 0.830 AC: 3990 AN: 4808

European-Finnish (FIN) AF: 0.950 AC: 9981 AN: 10508

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 63919 AN: 67944

Other (OTH) AF: 0.894 AC: 1886 AN: 2110

Alfa AF: 0.923 Hom.: 106282

Bravo AF: 0.872

Asia WGS AF: 0.804 AC: 2795 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.2
DANN	Benign	0.72
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs244465; hg19: chr5-142645903;