rs10034228

Variant names:

• chr4-111690594-T-C
• rs10034228
• ENST00000681719.1:n.352+19141T>C

Variant summary

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

The ENST00000681719.1(ENSG00000248656):​n.352+19141T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,024 control chromosomes in the GnomAD database, including 8,314 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 0.33 (8314 hom., cov: 32)
• Consequence: ENSG00000248656 ENST00000681719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444
• Publications: 18 publications found

Genes affected

ENSG00000248656 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248656	ENST00000681719.1	n.352+19141T>C		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49562 AN: 151906 Hom.: 8306 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.326 AC: 49581 AN: 152024 Hom.: 8314 Cov.: 32 AF XY: 0.328 AC XY: 24373 AN XY: 74312

African (AFR) AF: 0.357 AC: 14803 AN: 41470

American (AMR) AF: 0.345 AC: 5263 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2365 AN: 5160

South Asian (SAS) AF: 0.470 AC: 2262 AN: 4812

European-Finnish (FIN) AF: 0.240 AC: 2543 AN: 10576

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.301 AC: 20444 AN: 67950

Other (OTH) AF: 0.310 AC: 656 AN: 2114

Alfa AF: 0.317 Hom.: 27042

Bravo AF: 0.333

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs10034228; hg19: chr4-112611750;