4-87935581-C-T

Variant names:

• chr4-87935581-C-T
• rs10516796
• ENST00000829025.1:n.85+38058G>A

Variant summary

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

The ENST00000829025.1(ENSG00000307815):​n.85+38058G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,968 control chromosomes in the GnomAD database, including 23,776 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 0.55 (23776 hom., cov: 32)
• Consequence: ENSG00000307815 ENST00000829025.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 10 publications found

Genes affected

ENSG00000307815 (HGNC:58843):

ENSG00000307869 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829025.1. 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
	ENSG00000307815	ENST00000829025.1		n.85+38058G>A		intron	N/A
	ENSG00000307869	ENST00000829521.1		n.256-5487C>T		intron	N/A
	ENSG00000307869	ENST00000829522.1		n.458-5487C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83915 AN: 151850 Hom.: 23772 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.552 AC: 83948 AN: 151968 Hom.: 23776 Cov.: 32 AF XY: 0.558 AC XY: 41426 AN XY: 74270

African (AFR) AF: 0.411 AC: 17033 AN: 41416

American (AMR) AF: 0.566 AC: 8656 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2367 AN: 3470

East Asian (EAS) AF: 0.634 AC: 3281 AN: 5172

South Asian (SAS) AF: 0.670 AC: 3239 AN: 4834

European-Finnish (FIN) AF: 0.655 AC: 6888 AN: 10518

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.595 AC: 40441 AN: 67958

Other (OTH) AF: 0.562 AC: 1187 AN: 2112

Alfa AF: 0.589 Hom.: 13646

Bravo AF: 0.538

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10516796; hg19: chr4-88856733;