rs17194

Positions:

• chr13-84111092-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653443.1(ENSG00000288016):​n.196+24095C>T variant causes a intron, non coding transcript 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: ENST00000653443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000653443.1	n.196+24095C>T		intron_variant, non_coding_transcript_variant
	ENST00000691679.1	n.260-20328C>T		intron_variant, non_coding_transcript_variant
	ENST00000701394.1	n.253-9380C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.0947

Gnomad4 FIN AF: 0.0874

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.180

Alfa AF: 0.156 Hom.: 366

Bravo AF: 0.198

Asia WGS AF: 0.155 AC: 536 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17194; hg19: chr13-84685227;