rs10484819

Variant names:

• chr6-139536554-G-C
• rs10484819
• ENST00000647815.1:n.134+49939G>C

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+49939G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.044 in 152,272 control chromosomes in the GnomAD database, including 217 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 0.044 (217 hom., cov: 33)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0609 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
ENSG00000226571	ENST00000647815.1	n.134+49939G>C		intron_variant	Intron 1 of 2
ENSG00000226571	ENST00000648888.1	n.98+2138G>C		intron_variant	Intron 1 of 11

Frequencies

GnomAD3 genomes AF: 0.0441 AC: 6704 AN: 152154 Hom.: 216 Cov.: 33

Gnomad AFR AF: 0.0121

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.0291

Gnomad ASJ AF: 0.0897

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0732

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0440 AC: 6700 AN: 152272 Hom.: 217 Cov.: 33 AF XY: 0.0448 AC XY: 3333 AN XY: 74458

Gnomad4 AFR AF: 0.0120

Gnomad4 AMR AF: 0.0290

Gnomad4 ASJ AF: 0.0897

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0429

Gnomad4 FIN AF: 0.0732

Gnomad4 NFE AF: 0.0625

Gnomad4 OTH AF: 0.0493

Alfa AF: 0.0482 Hom.: 24

Bravo AF: 0.0405

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484819; hg19: chr6-139857691;