rs7222391

chr17-78330556-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000586321.1(ENSG00000267737):n.61-13409G>A variant causes a intron, non coding transcript 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: ENST00000586321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000586321.1	n.61-13409G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0831

Gnomad4 AMR AF: 0.0566

Gnomad4 ASJ AF: 0.0698

Gnomad4 EAS AF: 0.0770

Gnomad4 SAS AF: 0.0917

Gnomad4 FIN AF: 0.0444

Gnomad4 NFE AF: 0.0748

Gnomad4 OTH AF: 0.0764

Alfa AF: 0.0726 Hom.: 453

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7222391; hg19: chr17-76326637;