17-28222690-T-G

Variant names:

• chr17-28222690-T-G
• rs4435306
• ENST00000658960.1:n.828T>G

Variant summary

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

The ENST00000658960.1(ENSG00000287721):​n.828T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,982 control chromosomes in the GnomAD database, including 18,847 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 0.50 (18847 hom., cov: 31)
• Consequence: ENSG00000287721 ENST00000658960.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 7 publications found

Genes affected

ENSG00000287721 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371710	XR_007065684.1	n.74+5077A>C		intron_variant	Intron 1 of 2
LOC105371710	XR_007065685.1	n.74+5077A>C		intron_variant	Intron 1 of 2
LOC105371710	XR_934638.2	n.74+5077A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287721	ENST00000658960.1	n.828T>G		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000301334	ENST00000778049.1	n.341A>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000301334	ENST00000778042.1	n.97+5077A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75280 AN: 151862 Hom.: 18837 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.496 AC: 75328 AN: 151982 Hom.: 18847 Cov.: 31 AF XY: 0.496 AC XY: 36826 AN XY: 74266

African (AFR) AF: 0.440 AC: 18222 AN: 41440

American (AMR) AF: 0.437 AC: 6678 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1851 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2117 AN: 5148

South Asian (SAS) AF: 0.560 AC: 2698 AN: 4816

European-Finnish (FIN) AF: 0.543 AC: 5748 AN: 10578

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36157 AN: 67938

Other (OTH) AF: 0.523 AC: 1106 AN: 2114

Alfa AF: 0.507 Hom.: 28055

Bravo AF: 0.480

Asia WGS AF: 0.481 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs4435306; hg19: chr17-26549716;