chr5-143277248-A-G

Variant names:

• chr5-143277248-A-G
• rs258747
• ENST00000770709.1:n.118-7451A>G

Variant summary

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

The ENST00000770709.1(ENSG00000300303):​n.118-7451A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,010 control chromosomes in the GnomAD database, including 17,426 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 0.47 (17426 hom., cov: 32)
• Consequence: ENSG00000300303 ENST00000770709.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 25 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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.118-7451A>G		intron_variant	Intron 1 of 3
ENSG00000300303	ENST00000770710.1	n.118-7451A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71610 AN: 151892 Hom.: 17412 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.471 AC: 71661 AN: 152010 Hom.: 17426 Cov.: 32 AF XY: 0.465 AC XY: 34545 AN XY: 74290

African (AFR) AF: 0.419 AC: 17389 AN: 41460

American (AMR) AF: 0.382 AC: 5824 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1649 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1434 AN: 5188

South Asian (SAS) AF: 0.392 AC: 1890 AN: 4826

European-Finnish (FIN) AF: 0.502 AC: 5294 AN: 10552

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36478 AN: 67942

Other (OTH) AF: 0.461 AC: 973 AN: 2112

Alfa AF: 0.507 Hom.: 37078

Bravo AF: 0.461

Asia WGS AF: 0.370 AC: 1290 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.62
DANN	Benign	0.87
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs258747; hg19: chr5-142656813;