rs10413089

Positions:

• chr19-44952331-T-C

Variant summary

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

The ENST00000591646.1(ENSG00000267114):​n.114-1305A>G 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 0.21 in 152,190 control chromosomes in the GnomAD database, including 3,694 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 0.21 (3694 hom., cov: 32)
• Consequence: ENST00000591646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 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
	ENST00000591646.1	n.114-1305A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.210 AC: 32006 AN: 152072 Hom.: 3689 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.210 AC: 32031 AN: 152190 Hom.: 3694 Cov.: 32 AF XY: 0.210 AC XY: 15596 AN XY: 74402

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.0861

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.180

Alfa AF: 0.186 Hom.: 5771

Bravo AF: 0.215

Asia WGS AF: 0.206 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10413089; hg19: chr19-45455588;