rs17064578

Variant names:

• chr4-177300044-T-C
• rs17064578
• ENST00000763804.1:n.806A>G

Variant summary

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

The ENST00000763804.1(ENSG00000287544):​n.806A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,152 control chromosomes in the GnomAD database, including 2,905 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 (2905 hom., cov: 32)
• Consequence: ENSG00000287544 ENST00000763804.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 4 publications found

Genes affected

ENSG00000287544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377557	XR_001741925.2	n.234+1003A>G		intron_variant	Intron 1 of 2
LOC105377557	XR_007058380.1	n.234+1003A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287544	ENST00000763804.1	n.806A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000287544	ENST00000656694.1	n.112+1003A>G		intron_variant	Intron 1 of 4
ENSG00000287544	ENST00000662794.1	n.61+1003A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26445 AN: 152034 Hom.: 2890 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.174 AC: 26494 AN: 152152 Hom.: 2905 Cov.: 32 AF XY: 0.175 AC XY: 13029 AN XY: 74392

African (AFR) AF: 0.292 AC: 12123 AN: 41490

American (AMR) AF: 0.223 AC: 3404 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0594 AC: 206 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1502 AN: 5174

South Asian (SAS) AF: 0.116 AC: 562 AN: 4826

European-Finnish (FIN) AF: 0.125 AC: 1322 AN: 10606

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7001 AN: 67996

Other (OTH) AF: 0.144 AC: 304 AN: 2112

Alfa AF: 0.133 Hom.: 2451

Bravo AF: 0.188

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs17064578; hg19: chr4-178221198;