rs10012227

Variant names:

• chr4-18635692-G-A
• rs10012227
• ENST00000652661.1:n.614+6397G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-18635692-G-A
• chr4-18635692-G-T

Variant summary

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

The ENST00000652661.1(ENSG00000286046):​n.614+6397G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,164 control chromosomes in the GnomAD database, including 3,432 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 0.19 (3432 hom., cov: 32)
• Consequence: ENSG00000286046 ENST00000652661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 5 publications found

Genes affected

ENSG00000286046 (HGNC:59078):

LOC105374510 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652661.1. 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
	ENSG00000286046	ENST00000652661.1		n.614+6397G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28758 AN: 152044 Hom.: 3417 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.189 AC: 28788 AN: 152164 Hom.: 3432 Cov.: 32 AF XY: 0.194 AC XY: 14449 AN XY: 74388

African (AFR) AF: 0.126 AC: 5231 AN: 41528

American (AMR) AF: 0.374 AC: 5724 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 702 AN: 3466

East Asian (EAS) AF: 0.433 AC: 2241 AN: 5170

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4820

European-Finnish (FIN) AF: 0.139 AC: 1470 AN: 10586

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11410 AN: 67984

Other (OTH) AF: 0.179 AC: 379 AN: 2114

Alfa AF: 0.181 Hom.: 1445

Bravo AF: 0.208

Asia WGS AF: 0.333 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.72
PhyloP100		-0.022

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: rs10012227;

hg19: chr4-18637315;