chr5-130768383-A-C

Variant names:

• chr5-130768383-A-C
• rs10051722
• ENST00000661392.1:n.348+30156T>G

Variant summary

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

The ENST00000661392.1(ENSG00000287390):​n.348+30156T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,028 control chromosomes in the GnomAD database, including 8,974 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 0.34 (8974 hom., cov: 32)
• Consequence: ENSG00000287390 ENST00000661392.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 14 publications found

Genes affected

ENSG00000287390 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661392.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287390	ENST00000661392.1		n.348+30156T>G		intron	N/A
	ENSG00000287390	ENST00000804525.1		n.450+30156T>G		intron	N/A
	ENSG00000287390	ENST00000804527.1		n.469+30156T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51622 AN: 151910 Hom.: 8947 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.340 AC: 51702 AN: 152028 Hom.: 8974 Cov.: 32 AF XY: 0.346 AC XY: 25702 AN XY: 74328

African (AFR) AF: 0.360 AC: 14914 AN: 41478

American (AMR) AF: 0.397 AC: 6056 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1107 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2252 AN: 5178

South Asian (SAS) AF: 0.397 AC: 1912 AN: 4816

European-Finnish (FIN) AF: 0.362 AC: 3819 AN: 10554

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20749 AN: 67962

Other (OTH) AF: 0.335 AC: 704 AN: 2102

Alfa AF: 0.321 Hom.: 8645

Bravo AF: 0.342

Asia WGS AF: 0.453 AC: 1575 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.48
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10051722; hg19: chr5-130104076;