17-40461852-T-C

Variant names:

• chr17-40461852-T-C
• rs7214466
• ENST00000809097.1:n.197-1128A>G

Variant summary

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

The ENST00000809097.1(ENSG00000305154):​n.197-1128A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,952 control chromosomes in the GnomAD database, including 11,830 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 0.38 (11830 hom., cov: 32)
• Consequence: ENSG00000305154 ENST00000809097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47
• Publications: 7 publications found

Genes affected

ENSG00000305154 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809097.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305154	ENST00000809097.1		n.197-1128A>G		intron	N/A
	ENSG00000305154	ENST00000809098.1		n.194-1128A>G		intron	N/A
	ENSG00000305154	ENST00000809099.1		n.193-1128A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58368 AN: 151832 Hom.: 11821 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.384 AC: 58415 AN: 151952 Hom.: 11830 Cov.: 32 AF XY: 0.390 AC XY: 28956 AN XY: 74292

African (AFR) AF: 0.529 AC: 21881 AN: 41402

American (AMR) AF: 0.408 AC: 6226 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2097 AN: 5154

South Asian (SAS) AF: 0.353 AC: 1698 AN: 4810

European-Finnish (FIN) AF: 0.348 AC: 3681 AN: 10576

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20479 AN: 67950

Other (OTH) AF: 0.342 AC: 722 AN: 2114

Alfa AF: 0.296 Hom.: 3543

Bravo AF: 0.396

Asia WGS AF: 0.356 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.58
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs7214466; hg19: chr17-38618104;