rs10958704

Variant names:

• chr8-38470784-A-G
• rs10958704
• ENST00000812829.1:n.66+4223A>G

Variant summary

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

The ENST00000812829.1(ENSG00000305763):​n.66+4223A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,036 control chromosomes in the GnomAD database, including 9,779 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 0.35 (9779 hom., cov: 32)
• Consequence: ENSG00000305763 ENST00000812829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 14 publications found

Genes affected

ENSG00000305763 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812829.1. 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
	ENSG00000305763	ENST00000812829.1		n.66+4223A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53379 AN: 151918 Hom.: 9771 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.351 AC: 53393 AN: 152036 Hom.: 9779 Cov.: 32 AF XY: 0.353 AC XY: 26238 AN XY: 74310

African (AFR) AF: 0.257 AC: 10639 AN: 41452

American (AMR) AF: 0.281 AC: 4284 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3466

East Asian (EAS) AF: 0.350 AC: 1815 AN: 5180

South Asian (SAS) AF: 0.513 AC: 2476 AN: 4822

European-Finnish (FIN) AF: 0.390 AC: 4121 AN: 10560

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27657 AN: 67974

Other (OTH) AF: 0.332 AC: 701 AN: 2112

Alfa AF: 0.391 Hom.: 5617

Bravo AF: 0.333

Asia WGS AF: 0.430 AC: 1494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.32
PhyloP100		0.10

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: rs10958704;

hg19: chr8-38328302;