rs10484810

Variant names:

• chr6-139963540-C-A
• rs10484810
• ENST00000666152.2: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 ENST00000666152.2(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 ENST00000666152.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 1 publications found

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	ENST00000666152.2	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

African (AFR) AF: 0.303 AC: 12548 AN: 41472

American (AMR) AF: 0.0578 AC: 884 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3466

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0409 AC: 197 AN: 4818

European-Finnish (FIN) AF: 0.0542 AC: 574 AN: 10598

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0268 AC: 1821 AN: 68012

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10484810; hg19: chr6-140284677;