rs17111750

Positions:

• chr14-20442249-C-T

Variant summary

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

The ENST00000700970.1(ENSG00000291038):​n.693+141C>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 0.3 in 151,978 control chromosomes in the GnomAD database, including 7,034 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 0.30 (7034 hom., cov: 32)
• Consequence: ENST00000700970.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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 (SAS) allele frequency at 95% confidence interval = 0.36 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
	ENST00000700970.1	n.693+141C>T		intron_variant, non_coding_transcript_variant
	ENST00000687238.1	n.915+141C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45536 AN: 151860 Hom.: 7029 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.300 AC: 45570 AN: 151978 Hom.: 7034 Cov.: 32 AF XY: 0.302 AC XY: 22423 AN XY: 74264

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.319

Alfa AF: 0.303 Hom.: 1711

Bravo AF: 0.289

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17111750; hg19: chr14-20910408;