chr5-143277456-G-A

Variant names:

• chr5-143277456-G-A
• rs17287758
• ENST00000770709.1:n.118-7243G>A

Variant summary

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

The ENST00000770709.1(ENSG00000300303):​n.118-7243G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,140 control chromosomes in the GnomAD database, including 1,462 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 0.13 (1462 hom., cov: 32)
• Consequence: ENSG00000300303 ENST00000770709.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 11 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770709.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300303	ENST00000770709.1		n.118-7243G>A		intron	N/A
	ENSG00000300303	ENST00000770710.1		n.118-7243G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19587 AN: 152022 Hom.: 1468 Cov.: 32

Gnomad AFR AF: 0.0894

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.129 AC: 19577 AN: 152140 Hom.: 1462 Cov.: 32 AF XY: 0.124 AC XY: 9254 AN XY: 74368

African (AFR) AF: 0.0892 AC: 3704 AN: 41514

American (AMR) AF: 0.114 AC: 1741 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5182

South Asian (SAS) AF: 0.157 AC: 756 AN: 4824

European-Finnish (FIN) AF: 0.0778 AC: 823 AN: 10582

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11263 AN: 67976

Other (OTH) AF: 0.148 AC: 313 AN: 2110

Alfa AF: 0.156 Hom.: 3004

Bravo AF: 0.128

Asia WGS AF: 0.0760 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.53
DANN	Benign	0.61
PhyloP100		-0.60

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17287758;

hg19: chr5-142657021;