7-120173815-C-T

Variant names:

• chr7-120173815-C-T
• rs2190184
• ENST00000421825.2:n.188+5421C>T

Variant summary

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

The ENST00000421825.2(ENSG00000233969):​n.188+5421C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,012 control chromosomes in the GnomAD database, including 17,392 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 0.41 (17392 hom., cov: 32)
• Consequence: ENSG00000233969 ENST00000421825.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 6 publications found

Genes affected

ENSG00000233969 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 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
ENSG00000233969	ENST00000421825.2	n.188+5421C>T		intron_variant	Intron 2 of 3	3
ENSG00000233417	ENST00000456062.2	n.136-30719G>A		intron_variant	Intron 1 of 2	3
ENSG00000233417	ENST00000723829.1	n.259-32612G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62392 AN: 151892 Hom.: 17348 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.411 AC: 62489 AN: 152012 Hom.: 17392 Cov.: 32 AF XY: 0.402 AC XY: 29897 AN XY: 74292

African (AFR) AF: 0.786 AC: 32607 AN: 41490

American (AMR) AF: 0.327 AC: 4988 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3470

East Asian (EAS) AF: 0.588 AC: 3034 AN: 5160

South Asian (SAS) AF: 0.160 AC: 771 AN: 4818

European-Finnish (FIN) AF: 0.213 AC: 2255 AN: 10564

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16835 AN: 67934

Other (OTH) AF: 0.376 AC: 795 AN: 2114

Alfa AF: 0.281 Hom.: 12228

Bravo AF: 0.440

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.33
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2190184; hg19: chr7-119813869;