chr6-139536554-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647815.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226571	ENST00000647815.1		n.134+49939G>C		intron	N/A
	ENSG00000226571	ENST00000648888.1		n.98+2138G>C		intron	N/A
	ENSG00000226571	ENST00000775574.1		n.194-10688G>C		intron	N/A

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

African (AFR) AF: 0.0120 AC: 500 AN: 41568

American (AMR) AF: 0.0290 AC: 444 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0897 AC: 311 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0429 AC: 207 AN: 4826

European-Finnish (FIN) AF: 0.0732 AC: 776 AN: 10594

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0625 AC: 4248 AN: 68020

Other (OTH) AF: 0.0493 AC: 104 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.67
PhyloP100		-0.071

Splicing

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

Other links and lift over

dbSNP: rs10484819; hg19: chr6-139857691;