rs16890720

chr6-79422575-G-A

Variant summary

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

The ENST00000652956.1(ENSG00000231533):n.184+372G>A 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 0.174 in 151,976 control chromosomes in the GnomAD database, including 2,609 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 0.17 (2609 hom., cov: 32)
• Consequence: ENST00000652956.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506851	XR_001744215.3	n.1825+372G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652956.1	n.184+372G>A		intron_variant, non_coding_transcript_variant
	ENST00000654165.1	n.1898G>A		non_coding_transcript_exon_variant	2/2
	ENST00000653204.1	n.526+1387G>A		intron_variant, non_coding_transcript_variant
	ENST00000653689.1	n.1497+372G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26368 AN: 151858 Hom.: 2612 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0687

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.174 AC: 26376 AN: 151976 Hom.: 2609 Cov.: 32 AF XY: 0.168 AC XY: 12461 AN XY: 74332

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0687

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.180

Alfa AF: 0.162 Hom.: 1688

Bravo AF: 0.186

Asia WGS AF: 0.125 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.0
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: rs16890720; hg19: chr6-80132292;