chr10-4041651-C-G

Variant names:

• chr10-4041651-C-G
• rs2935283
• ENST00000656775.1:n.690-5430C>G

Variant summary

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

The NR_176060.1(LOC107984195):​n.613+9948C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0346 in 152,210 control chromosomes in the GnomAD database, including 250 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 0.035 (250 hom., cov: 32)
• Consequence: LOC107984195 NR_176060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_176060.1. 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
	LOC107984195	NR_176060.1		n.613+9948C>G		intron	N/A
	LOC107984195	NR_176062.1		n.613+9948C>G		intron	N/A
	LOC107984195	NR_176063.1		n.868-5430C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227101	ENST00000656775.1		n.690-5430C>G		intron	N/A
	ENSG00000227101	ENST00000658139.1		n.569-5430C>G		intron	N/A
	ENSG00000227101	ENST00000667089.1		n.628-9819C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0344 AC: 5229 AN: 152092 Hom.: 244 Cov.: 32

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0174

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00578

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0346 AC: 5270 AN: 152210 Hom.: 250 Cov.: 32 AF XY: 0.0342 AC XY: 2546 AN XY: 74422

African (AFR) AF: 0.0813 AC: 3376 AN: 41520

American (AMR) AF: 0.0173 AC: 265 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3470

East Asian (EAS) AF: 0.182 AC: 940 AN: 5174

South Asian (SAS) AF: 0.0203 AC: 98 AN: 4826

European-Finnish (FIN) AF: 0.0109 AC: 116 AN: 10596

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00578 AC: 393 AN: 68022

Other (OTH) AF: 0.0326 AC: 69 AN: 2114

Alfa AF: 0.00180 Hom.: 0

Bravo AF: 0.0387

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.41
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2935283; hg19: chr10-4083843;