5-16256271-A-G

Variant names:

• chr5-16256271-A-G
• rs7730897
• ENST00000780293.1:n.242-14362T>C

Variant summary

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

The ENST00000780293.1(ENSG00000301626):​n.242-14362T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,124 control chromosomes in the GnomAD database, including 54,653 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 0.84 (54653 hom., cov: 32)
• Consequence: ENSG00000301626 ENST00000780293.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 2 publications found

Genes affected

ENSG00000301626 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 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
ENSG00000301626	ENST00000780293.1	n.242-14362T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128074 AN: 152006 Hom.: 54630 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.842 AC: 128147 AN: 152124 Hom.: 54653 Cov.: 32 AF XY: 0.842 AC XY: 62598 AN XY: 74346

African (AFR) AF: 0.686 AC: 28455 AN: 41458

American (AMR) AF: 0.910 AC: 13904 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2933 AN: 3472

East Asian (EAS) AF: 0.949 AC: 4887 AN: 5152

South Asian (SAS) AF: 0.821 AC: 3952 AN: 4816

European-Finnish (FIN) AF: 0.881 AC: 9345 AN: 10608

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61815 AN: 68014

Other (OTH) AF: 0.838 AC: 1773 AN: 2116

Alfa AF: 0.877 Hom.: 35451

Bravo AF: 0.837

Asia WGS AF: 0.837 AC: 2912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.74
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs7730897; hg19: chr5-16256380;