rs162859

Variant names:

• chr5-16444840-A-G
• rs162859
• ENST00000773338.1:n.429+2551A>G

Variant summary

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

The ENST00000773338.1(ENSG00000300672):​n.429+2551A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,140 control chromosomes in the GnomAD database, including 33,632 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 0.66 (33632 hom., cov: 33)
• Consequence: ENSG00000300672 ENST00000773338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 5 publications found

Genes affected

ENSG00000300672 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 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
ENSG00000300672	ENST00000773338.1	n.429+2551A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100792 AN: 152020 Hom.: 33608 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.663 AC: 100878 AN: 152140 Hom.: 33632 Cov.: 33 AF XY: 0.662 AC XY: 49237 AN XY: 74396

African (AFR) AF: 0.622 AC: 25790 AN: 41488

American (AMR) AF: 0.657 AC: 10046 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2382 AN: 3472

East Asian (EAS) AF: 0.467 AC: 2416 AN: 5168

South Asian (SAS) AF: 0.544 AC: 2622 AN: 4816

European-Finnish (FIN) AF: 0.760 AC: 8048 AN: 10594

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47456 AN: 68000

Other (OTH) AF: 0.664 AC: 1402 AN: 2112

Alfa AF: 0.685 Hom.: 17024

Bravo AF: 0.655

Asia WGS AF: 0.538 AC: 1866 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.51
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs162859; hg19: chr5-16444949;