rs10516800

Variant names:

• chr4-87970438-G-C
• rs10516800
• ENST00000829025.1:n.85+3201C>G

Variant summary

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

The ENST00000829025.1(ENSG00000307815):​n.85+3201C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,082 control chromosomes in the GnomAD database, including 5,609 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 0.27 (5609 hom., cov: 32)
• Consequence: ENSG00000307815 ENST00000829025.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 7 publications found

Genes affected

ENSG00000307815 (HGNC:58843):

LOC124900730 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 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+3201C>G		intron	N/A
	ENSG00000307815	ENST00000829040.1		n.105+3201C>G		intron	N/A
	ENSG00000307815	ENST00000829041.1		n.96+3201C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40941 AN: 151964 Hom.: 5606 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.269 AC: 40979 AN: 152082 Hom.: 5609 Cov.: 32 AF XY: 0.275 AC XY: 20467 AN XY: 74342

African (AFR) AF: 0.265 AC: 11000 AN: 41494

American (AMR) AF: 0.282 AC: 4313 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 844 AN: 3460

East Asian (EAS) AF: 0.370 AC: 1914 AN: 5166

South Asian (SAS) AF: 0.206 AC: 995 AN: 4820

European-Finnish (FIN) AF: 0.355 AC: 3749 AN: 10568

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17142 AN: 67980

Other (OTH) AF: 0.278 AC: 587 AN: 2108

Alfa AF: 0.264 Hom.: 699

Bravo AF: 0.262

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.44
PhyloP100		-0.79

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: rs10516800;

hg19: chr4-88891590;