rs322185

Variant names:

• chr17-27378727-C-T
• rs322185
• ENST00000728376.1:n.223+25693G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000728376.1(ENSG00000295161):​n.223+25693G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,980 control chromosomes in the GnomAD database, including 31,612 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 0.64 (31612 hom., cov: 32)
• Consequence: ENSG00000295161 ENST00000728376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 1 publications found

Genes affected

ENSG00000295161 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 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
ENSG00000295161	ENST00000728376.1	n.223+25693G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97632 AN: 151862 Hom.: 31576 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.643 AC: 97731 AN: 151980 Hom.: 31612 Cov.: 32 AF XY: 0.643 AC XY: 47756 AN XY: 74280

African (AFR) AF: 0.693 AC: 28713 AN: 41440

American (AMR) AF: 0.583 AC: 8899 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2264 AN: 3472

East Asian (EAS) AF: 0.692 AC: 3584 AN: 5182

South Asian (SAS) AF: 0.554 AC: 2656 AN: 4796

European-Finnish (FIN) AF: 0.674 AC: 7124 AN: 10564

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42311 AN: 67954

Other (OTH) AF: 0.646 AC: 1366 AN: 2114

Alfa AF: 0.633 Hom.: 3800

Bravo AF: 0.639

Asia WGS AF: 0.616 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	6.9
DANN	Benign	0.78
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs322185; hg19: chr17-25705753;