chr17-78330556-G-A

Variant names:

• chr17-78330556-G-A
• rs7222391
• ENST00000586321.1:n.61-13409G>A

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.61-13409G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0735 in 151,990 control chromosomes in the GnomAD database, including 453 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 0.073 (453 hom., cov: 31)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894
• Publications: 4 publications found

Genes affected

ENSG00000267737 (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 (SAS) allele frequency at 95% confidence interval = 0.0847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371912	NR_188632.1	n.74-13409G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267737	ENST00000586321.1	n.61-13409G>A		intron_variant	Intron 1 of 2	3
ENSG00000267737	ENST00000823930.1	n.39-13409G>A		intron_variant	Intron 1 of 1
ENSG00000267737	ENST00000823931.1	n.71+12568G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0734 AC: 11150 AN: 151872 Hom.: 451 Cov.: 31

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.0698

Gnomad EAS AF: 0.0769

Gnomad SAS AF: 0.0908

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.0768

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

GnomAD4 genome AF: 0.0735 AC: 11167 AN: 151990 Hom.: 453 Cov.: 31 AF XY: 0.0723 AC XY: 5368 AN XY: 74256

African (AFR) AF: 0.0831 AC: 3441 AN: 41418

American (AMR) AF: 0.0566 AC: 864 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0698 AC: 242 AN: 3468

East Asian (EAS) AF: 0.0770 AC: 398 AN: 5166

South Asian (SAS) AF: 0.0917 AC: 441 AN: 4808

European-Finnish (FIN) AF: 0.0444 AC: 469 AN: 10554

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0748 AC: 5088 AN: 67994

Other (OTH) AF: 0.0764 AC: 161 AN: 2106

Alfa AF: 0.0729 Hom.: 657

Bravo AF: 0.0732

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.64
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs7222391; hg19: chr17-76326637;