rs17145184

Variant names:

• chr7-68176128-T-C
• rs17145184
• ENST00000446187.2:n.465+8662A>G

Variant summary

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

The NR_187905.1(LOC105375341):​n.523+8662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,198 control chromosomes in the GnomAD database, including 2,226 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 0.15 (2226 hom., cov: 32)
• Consequence: LOC105375341 NR_187905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820
• Publications: 1 publications found

Genes affected

ENSG00000226829 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187905.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375341	NR_187905.1		n.523+8662A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226829	ENST00000446187.2	TSL:5	n.465+8662A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23462 AN: 152080 Hom.: 2204 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0977

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.155 AC: 23534 AN: 152198 Hom.: 2226 Cov.: 32 AF XY: 0.158 AC XY: 11763 AN XY: 74416

African (AFR) AF: 0.261 AC: 10833 AN: 41508

American (AMR) AF: 0.139 AC: 2120 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0746 AC: 259 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1052 AN: 5174

South Asian (SAS) AF: 0.175 AC: 843 AN: 4826

European-Finnish (FIN) AF: 0.118 AC: 1253 AN: 10608

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0977 AC: 6647 AN: 68008

Other (OTH) AF: 0.143 AC: 303 AN: 2116

Alfa AF: 0.115 Hom.: 4724

Bravo AF: 0.158

Asia WGS AF: 0.187 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.57
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs17145184; hg19: chr7-67641115;