rs6088466

Variant names:

• chr20-34325728-G-A
• rs6088466
• ENST00000743410.1:n.79-7849C>T

Variant summary

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

The ENST00000743410.1(ENSG00000296893):​n.79-7849C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,964 control chromosomes in the GnomAD database, including 6,746 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 (6746 hom., cov: 31)
• Consequence: ENSG00000296893 ENST00000743410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 23 publications found

Genes affected

ENSG00000296893 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 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
ENSG00000296893	ENST00000743410.1	n.79-7849C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40077 AN: 151846 Hom.: 6731 Cov.: 31

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.264 AC: 40104 AN: 151964 Hom.: 6746 Cov.: 31 AF XY: 0.267 AC XY: 19804 AN XY: 74274

African (AFR) AF: 0.0726 AC: 3010 AN: 41470

American (AMR) AF: 0.480 AC: 7321 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3466

East Asian (EAS) AF: 0.420 AC: 2163 AN: 5144

South Asian (SAS) AF: 0.190 AC: 915 AN: 4812

European-Finnish (FIN) AF: 0.300 AC: 3164 AN: 10558

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21227 AN: 67944

Other (OTH) AF: 0.308 AC: 650 AN: 2112

Alfa AF: 0.306 Hom.: 24525

Bravo AF: 0.277

Asia WGS AF: 0.306 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.36
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs6088466; hg19: chr20-32913534;