chr10-4014679-G-A

Variant names:

• chr10-4014679-G-A
• rs10508272
• ENST00000846922.1:n.281-2295G>A

Variant summary

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

The ENST00000846922.1(ENSG00000227101):​n.281-2295G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 152,178 control chromosomes in the GnomAD database, including 278 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 0.054 (278 hom., cov: 33)
• Consequence: ENSG00000227101 ENST00000846922.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 4 publications found

Genes affected

ENSG00000227101 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846922.1. 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
	ENSG00000227101	ENST00000846922.1		n.281-2295G>A		intron	N/A
	ENSG00000227101	ENST00000846923.1		n.249+9986G>A		intron	N/A
	ENSG00000227101	ENST00000846927.1		n.230-2295G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0540 AC: 8208 AN: 152060 Hom.: 279 Cov.: 33

Gnomad AFR AF: 0.0379

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0603

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0539 AC: 8210 AN: 152178 Hom.: 278 Cov.: 33 AF XY: 0.0531 AC XY: 3952 AN XY: 74376

African (AFR) AF: 0.0380 AC: 1576 AN: 41510

American (AMR) AF: 0.0476 AC: 727 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0697 AC: 242 AN: 3472

East Asian (EAS) AF: 0.157 AC: 813 AN: 5182

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4822

European-Finnish (FIN) AF: 0.0227 AC: 240 AN: 10586

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0603 AC: 4101 AN: 67998

Other (OTH) AF: 0.0587 AC: 124 AN: 2114

Alfa AF: 0.0585 Hom.: 244

Bravo AF: 0.0562

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.020
DANN	Benign	0.39
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10508272; hg19: chr10-4056871;