rs10484819

Positions:

• chr6-139536554-G-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, non coding transcript 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: ENST00000647815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000647815.1	n.134+49939G>C		intron_variant, non_coding_transcript_variant
	ENST00000648888.1	n.98+2138G>C		intron_variant, non_coding_transcript_variant

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;