rs175990

chr14-76942722-A-Cchr14-76942722-A-T

Variant summary

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

The ENST00000692498.1(ENSG00000288762):n.117+5922T>G 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 0.224 in 152,078 control chromosomes in the GnomAD database, including 4,095 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 0.22 (4095 hom., cov: 31)
• Consequence: ENST00000692498.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692498.1	n.117+5922T>G		intron_variant, non_coding_transcript_variant
	ENST00000688632.1	n.84+5922T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34104 AN: 151960 Hom.: 4098 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.224 AC: 34098 AN: 152078 Hom.: 4095 Cov.: 31 AF XY: 0.223 AC XY: 16597 AN XY: 74362

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.244

Alfa AF: 0.271 Hom.: 7640

Bravo AF: 0.226

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	9.5
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs175990; hg19: chr14-77409065;