chr6-160678471-G-A

Variant names:

• chr6-160678471-G-A
• rs5014650
• ENST00000797429.1:n.111+577C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000797429.1(ENSG00000303834):​n.111+577C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,104 control chromosomes in the GnomAD database, including 1,867 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 0.15 (1867 hom., cov: 31)
• Consequence: ENSG00000303834 ENST00000797429.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 8 publications found

Genes affected

ENSG00000303834 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303834	ENST00000797429.1	n.111+577C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23224 AN: 151986 Hom.: 1860 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00463

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.153 AC: 23252 AN: 152104 Hom.: 1867 Cov.: 31 AF XY: 0.149 AC XY: 11074 AN XY: 74356

African (AFR) AF: 0.175 AC: 7244 AN: 41486

American (AMR) AF: 0.137 AC: 2093 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3468

East Asian (EAS) AF: 0.00464 AC: 24 AN: 5174

South Asian (SAS) AF: 0.119 AC: 575 AN: 4826

European-Finnish (FIN) AF: 0.114 AC: 1209 AN: 10580

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11034 AN: 67990

Other (OTH) AF: 0.134 AC: 284 AN: 2112

Alfa AF: 0.153 Hom.: 1413

Bravo AF: 0.154

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.60
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs5014650; hg19: chr6-161099503;