rs853356

chr6-14173197-G-A

Variant summary

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

The ENST00000650535.1(ENSG00000285639):n.107-18487C>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 0.26 in 151,954 control chromosomes in the GnomAD database, including 5,799 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 0.26 (5799 hom., cov: 32)
• Consequence: ENST00000650535.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 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
	ENST00000650535.1	n.107-18487C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39453 AN: 151836 Hom.: 5786 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.260 AC: 39501 AN: 151954 Hom.: 5799 Cov.: 32 AF XY: 0.264 AC XY: 19636 AN XY: 74260

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.269

Alfa AF: 0.227 Hom.: 1652

Bravo AF: 0.262

Asia WGS AF: 0.535 AC: 1857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.4
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs853356; hg19: chr6-14173428;