rs10034228

Positions:

• chr4-111690594-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000681719.1(ENSG00000248656):​n.352+19141T>C variant causes a intron, non coding transcript 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: ENST00000681719.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000681719.1	n.352+19141T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.310

Alfa AF: 0.314 Hom.: 11754

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10034228; hg19: chr4-112611750;