chr10-29807699-A-G

Variant names:

• chr10-29807699-A-G
• rs2986971
• ENST00000795177.1:n.100-5415A>G

Variant summary

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

The ENST00000795177.1(ENSG00000303513):​n.100-5415A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,052 control chromosomes in the GnomAD database, including 18,295 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 0.49 (18295 hom., cov: 31)
• Consequence: ENSG00000303513 ENST00000795177.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 13 publications found

Genes affected

ENSG00000303513 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795177.1. 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
	ENSG00000303513	ENST00000795177.1		n.100-5415A>G		intron	N/A
	ENSG00000303513	ENST00000795178.1		n.95+3799A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73937 AN: 151934 Hom.: 18287 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.487 AC: 73982 AN: 152052 Hom.: 18295 Cov.: 31 AF XY: 0.478 AC XY: 35558 AN XY: 74330

African (AFR) AF: 0.533 AC: 22099 AN: 41478

American (AMR) AF: 0.418 AC: 6386 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1812 AN: 3470

East Asian (EAS) AF: 0.551 AC: 2840 AN: 5156

South Asian (SAS) AF: 0.482 AC: 2323 AN: 4818

European-Finnish (FIN) AF: 0.362 AC: 3830 AN: 10574

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32774 AN: 67954

Other (OTH) AF: 0.520 AC: 1098 AN: 2112

Alfa AF: 0.490 Hom.: 67251

Bravo AF: 0.496

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.49
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs2986971; hg19: chr10-30096628;