rs17194

Variant names:

• chr13-84111092-C-T
• rs17194
• ENST00000653443.1:n.196+24095C>T

Variant summary

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

The ENST00000653443.1(ENSG00000288016):​n.196+24095C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,074 control chromosomes in the GnomAD database, including 3,348 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 0.18 (3348 hom., cov: 32)
• Consequence: ENSG00000288016 ENST00000653443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 0 publications found

Genes affected

ENSG00000288016 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653443.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288016	ENST00000653443.1		n.196+24095C>T		intron	N/A
	ENSG00000288016	ENST00000691679.2		n.262-20328C>T		intron	N/A
	ENSG00000288016	ENST00000701394.1		n.253-9380C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27536 AN: 151956 Hom.: 3328 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.0874

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.182 AC: 27611 AN: 152074 Hom.: 3348 Cov.: 32 AF XY: 0.181 AC XY: 13452 AN XY: 74344

African (AFR) AF: 0.341 AC: 14154 AN: 41470

American (AMR) AF: 0.199 AC: 3039 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 489 AN: 3472

East Asian (EAS) AF: 0.212 AC: 1092 AN: 5150

South Asian (SAS) AF: 0.0947 AC: 456 AN: 4814

European-Finnish (FIN) AF: 0.0874 AC: 926 AN: 10596

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6988 AN: 67974

Other (OTH) AF: 0.180 AC: 380 AN: 2110

Alfa AF: 0.161 Hom.: 408

Bravo AF: 0.198

Asia WGS AF: 0.155 AC: 536 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.39
PhyloP100		0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17194;

hg19: chr13-84685227;