17-70293941-C-T

Variant names:

• chr17-70293941-C-T
• rs11077488
• ENST00000771979.1:n.145+1387C>T

Variant summary

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

The ENST00000771979.1(ENSG00000300458):​n.145+1387C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,048 control chromosomes in the GnomAD database, including 1,587 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 0.14 (1587 hom., cov: 32)
• Consequence: ENSG00000300458 ENST00000771979.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 5 publications found

Genes affected

ENSG00000300458 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 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
ENSG00000300458	ENST00000771979.1	n.145+1387C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21055 AN: 151932 Hom.: 1586 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.139 AC: 21066 AN: 152048 Hom.: 1587 Cov.: 32 AF XY: 0.137 AC XY: 10170 AN XY: 74316

African (AFR) AF: 0.112 AC: 4649 AN: 41476

American (AMR) AF: 0.164 AC: 2504 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3468

East Asian (EAS) AF: 0.169 AC: 873 AN: 5164

South Asian (SAS) AF: 0.147 AC: 707 AN: 4822

European-Finnish (FIN) AF: 0.0859 AC: 908 AN: 10568

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10121 AN: 67964

Other (OTH) AF: 0.175 AC: 369 AN: 2114

Alfa AF: 0.146 Hom.: 1500

Bravo AF: 0.142

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.65
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs11077488; hg19: chr17-68290082;