10-6882482-C-A

Position:

• chr10-6882482-C-A

Variant summary

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

The ENST00000664549.1(ENSG00000287277):​n.568+52631G>T 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 0.108 in 143,180 control chromosomes in the GnomAD database, including 967 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 0.11 (967 hom., cov: 29)
• Consequence: ENST00000664549.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376387	XR_007062046.1	n.852-18348G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664549.1	n.568+52631G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.108 AC: 15481 AN: 143078 Hom.: 967 Cov.: 29

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0460

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.0563

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.0777

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0742

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.108 AC: 15491 AN: 143180 Hom.: 967 Cov.: 29 AF XY: 0.109 AC XY: 7599 AN XY: 69752

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.0563

Gnomad4 EAS AF: 0.00117

Gnomad4 SAS AF: 0.0775

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.0848

Gnomad4 OTH AF: 0.0840

Alfa AF: 0.0266 Hom.: 20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11816922; hg19: chr10-6924444;