chr17-28274107-T-G

Variant names:

• chr17-28274107-T-G
• rs2006933
• ENST00000703576.1:n.360+981A>C

Variant summary

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

The ENST00000703576.1(ENSG00000260777):​n.360+981A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,140 control chromosomes in the GnomAD database, including 4,051 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 0.23 (4051 hom., cov: 32)
• Consequence: ENSG00000260777 ENST00000703576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 8 publications found

Genes affected

ENSG00000260777 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703576.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260777	ENST00000703576.1		n.360+981A>C		intron	N/A
	ENSG00000260777	ENST00000703577.1		n.872+981A>C		intron	N/A
	ENSG00000260777	ENST00000703578.1		n.887+981A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34641 AN: 152022 Hom.: 4044 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.228 AC: 34675 AN: 152140 Hom.: 4051 Cov.: 32 AF XY: 0.227 AC XY: 16904 AN XY: 74382

African (AFR) AF: 0.209 AC: 8676 AN: 41514

American (AMR) AF: 0.212 AC: 3243 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1672 AN: 5180

South Asian (SAS) AF: 0.339 AC: 1635 AN: 4818

European-Finnish (FIN) AF: 0.173 AC: 1828 AN: 10588

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15955 AN: 67982

Other (OTH) AF: 0.244 AC: 515 AN: 2114

Alfa AF: 0.224 Hom.: 3676

Bravo AF: 0.228

Asia WGS AF: 0.357 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.32
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs2006933; hg19: chr17-26601133;