rs10484810

Variant names:

• chr6-139963540-C-A
• rs10484810
• ENST00000666152.1:n.747+14472G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-139963540-C-A
• chr6-139963540-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000666152.1(ENSG00000287820):​n.747+14472G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,160 control chromosomes in the GnomAD database, including 1,992 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 (1992 hom., cov: 32)
• Consequence: ENSG00000287820 ENST00000666152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

Genes affected

ENSG00000287820 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287820	ENST00000666152.1	n.747+14472G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16348 AN: 152042 Hom.: 1997 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0268

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.108 AC: 16361 AN: 152160 Hom.: 1992 Cov.: 32 AF XY: 0.106 AC XY: 7903 AN XY: 74410

Gnomad4 AFR AF: 0.303 AC: 0.302566 AN: 0.302566

Gnomad4 AMR AF: 0.0578 AC: 0.057808 AN: 0.057808

Gnomad4 ASJ AF: 0.0277 AC: 0.0276976 AN: 0.0276976

Gnomad4 EAS AF: 0.000579 AC: 0.000578704 AN: 0.000578704

Gnomad4 SAS AF: 0.0409 AC: 0.0408883 AN: 0.0408883

Gnomad4 FIN AF: 0.0542 AC: 0.0541612 AN: 0.0541612

Gnomad4 NFE AF: 0.0268 AC: 0.0267747 AN: 0.0267747

Gnomad4 OTH AF: 0.0994 AC: 0.0994318 AN: 0.0994318

Alfa AF: 0.0426 Hom.: 211

Bravo AF: 0.117

Asia WGS AF: 0.0330 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484810; hg19: chr6-140284677;