5-101471764-G-T

Variant names:

• chr5-101471764-G-T
• rs10515309
• ENST00000780281.1:n.149-1078G>T

Variant summary

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

The ENST00000780281.1(ENSG00000301625):​n.149-1078G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0316 in 151,752 control chromosomes in the GnomAD database, including 184 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 0.032 (184 hom., cov: 32)
• Consequence: ENSG00000301625 ENST00000780281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 0 publications found

Genes affected

ENSG00000301625 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0877 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780281.1. 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
	ENSG00000301625	ENST00000780281.1		n.149-1078G>T		intron	N/A
	ENSG00000301625	ENST00000780282.1		n.153-207G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0316 AC: 4787 AN: 151634 Hom.: 183 Cov.: 32

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.00853

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0316 AC: 4794 AN: 151752 Hom.: 184 Cov.: 32 AF XY: 0.0312 AC XY: 2311 AN XY: 74170

African (AFR) AF: 0.0901 AC: 3733 AN: 41434

American (AMR) AF: 0.0202 AC: 306 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00374 AC: 18 AN: 4818

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10590

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.00853 AC: 578 AN: 67776

Other (OTH) AF: 0.0294 AC: 62 AN: 2108

Alfa AF: 0.0117 Hom.: 13

Bravo AF: 0.0357

Asia WGS AF: 0.00549 AC: 19 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.6
DANN	Benign	0.54
PhyloP100		0.041

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: rs10515309;

hg19: chr5-100807468;