10-102853598-A-G

Variant names:

• chr10-102853598-A-G
• rs12219246
• ENST00000440461.3:n.258+657T>C

Variant summary

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

The ENST00000440461.3(ENSG00000282772):​n.258+657T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 148,672 control chromosomes in the GnomAD database, including 10,671 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 0.37 (10671 hom., cov: 29)
• Consequence: ENSG00000282772 ENST00000440461.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 13 publications found

Genes affected

ENSG00000282772 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440461.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282772	ENST00000440461.3	TSL:5	n.258+657T>C		intron	N/A
	ENSG00000282772	ENST00000629474.2	TSL:5	n.259+657T>C		intron	N/A
	ENSG00000282772	ENST00000631443.1	TSL:4	n.259+657T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 55720 AN: 148642 Hom.: 10672 Cov.: 29

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.375 AC: 55727 AN: 148672 Hom.: 10671 Cov.: 29 AF XY: 0.373 AC XY: 27083 AN XY: 72530

African (AFR) AF: 0.365 AC: 14909 AN: 40822

American (AMR) AF: 0.380 AC: 5656 AN: 14884

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1432 AN: 3458

East Asian (EAS) AF: 0.559 AC: 2833 AN: 5070

South Asian (SAS) AF: 0.435 AC: 2069 AN: 4756

European-Finnish (FIN) AF: 0.302 AC: 2763 AN: 9156

Middle Eastern (MID) AF: 0.396 AC: 111 AN: 280

European-Non Finnish (NFE) AF: 0.371 AC: 24984 AN: 67302

Other (OTH) AF: 0.387 AC: 789 AN: 2040

Alfa AF: 0.381 Hom.: 1453

Bravo AF: 0.382

Asia WGS AF: 0.452 AC: 1566 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
DANN	Benign	0.16
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12219246; hg19: chr10-104613355;