chr5-155096973-T-A

Variant names:

• chr5-155096973-T-A
• rs10038971
• ENST00000660390.1:n.281+9263T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000660390.1(ENSG00000287963):​n.281+9263T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,088 control chromosomes in the GnomAD database, including 12,104 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 0.36 (12104 hom., cov: 32)
• Consequence: ENSG00000287963 ENST00000660390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 2 publications found

Genes affected

ENSG00000287963 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660390.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287963	ENST00000660390.1		n.281+9263T>A		intron	N/A
	ENSG00000287963	ENST00000668848.1		n.179+9263T>A		intron	N/A
	ENSG00000287963	ENST00000808202.1		n.122+5476T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55218 AN: 151970 Hom.: 12070 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.364 AC: 55300 AN: 152088 Hom.: 12104 Cov.: 32 AF XY: 0.367 AC XY: 27273 AN XY: 74362

African (AFR) AF: 0.619 AC: 25667 AN: 41468

American (AMR) AF: 0.240 AC: 3668 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 952 AN: 3472

East Asian (EAS) AF: 0.430 AC: 2229 AN: 5178

South Asian (SAS) AF: 0.382 AC: 1838 AN: 4816

European-Finnish (FIN) AF: 0.321 AC: 3400 AN: 10578

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.242 AC: 16478 AN: 67970

Other (OTH) AF: 0.349 AC: 737 AN: 2114

Alfa AF: 0.316 Hom.: 1123

Bravo AF: 0.369

Asia WGS AF: 0.391 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	14
DANN	Benign	0.78
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10038971; hg19: chr5-154476533;