rs2368416

chr10-29408056-T-C

Variant summary

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

The ENST00000658254.1(ENSG00000287402):n.1122+189A>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 0.516 in 151,412 control chromosomes in the GnomAD database, including 20,929 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 0.52 (20929 hom., cov: 30)
• Consequence: ENST00000658254.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376474	XR_930787.3	n.1209+189A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658254.1	n.1122+189A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78048 AN: 151294 Hom.: 20881 Cov.: 30

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.516 AC: 78157 AN: 151412 Hom.: 20929 Cov.: 30 AF XY: 0.524 AC XY: 38718 AN XY: 73892

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.483

Alfa AF: 0.499 Hom.: 3260

Bravo AF: 0.523

Asia WGS AF: 0.490 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.0
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2368416; hg19: chr10-29696985;