17-70808080-G-T

Variant names:

• chr17-70808080-G-T
• rs17764124
• ENST00000774266.1:n.246+85338G>T

Variant summary

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

The ENST00000774266.1(ENSG00000300827):​n.246+85338G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0685 in 152,084 control chromosomes in the GnomAD database, including 387 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 0.069 (387 hom., cov: 32)
• Consequence: ENSG00000300827 ENST00000774266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 0 publications found

Genes affected

ENSG00000300827 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774266.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300827	ENST00000774266.1		n.246+85338G>T		intron	N/A
	ENSG00000300827	ENST00000774267.1		n.185+85338G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0686 AC: 10418 AN: 151966 Hom.: 388 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0508

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0623

Gnomad FIN AF: 0.0660

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0685 AC: 10418 AN: 152084 Hom.: 387 Cov.: 32 AF XY: 0.0685 AC XY: 5094 AN XY: 74338

African (AFR) AF: 0.108 AC: 4462 AN: 41488

American (AMR) AF: 0.0507 AC: 773 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0432 AC: 150 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5168

South Asian (SAS) AF: 0.0626 AC: 302 AN: 4826

European-Finnish (FIN) AF: 0.0660 AC: 699 AN: 10588

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0563 AC: 3829 AN: 67986

Other (OTH) AF: 0.0653 AC: 138 AN: 2112

Alfa AF: 0.0598 Hom.: 393

Bravo AF: 0.0690

Asia WGS AF: 0.0230 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.48
PhyloP100		-0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17764124;

hg19: chr17-68804221;