10-5566239-C-T

Position:

• chr10-5566239-C-T

Variant summary

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

The ENST00000664654.1(ENSG00000287235):​n.346+297G>A 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 0.252 in 152,198 control chromosomes in the GnomAD database, including 5,676 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 0.25 (5676 hom., cov: 32)
• Consequence: ENST00000664654.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

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 (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376381	XR_001747274.2	n.346+297G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664654.1	n.346+297G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38407 AN: 152080 Hom.: 5677 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.0416

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.252 AC: 38426 AN: 152198 Hom.: 5676 Cov.: 32 AF XY: 0.253 AC XY: 18813 AN XY: 74394

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.0417

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.269

Alfa AF: 0.297 Hom.: 10367

Bravo AF: 0.239

Asia WGS AF: 0.132 AC: 461 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	5.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7899101; hg19: chr10-5608202; COSMIC: COSV66929888;