6-54683511-G-A

Variant names:

• chr6-54683511-G-A
• rs10484990
• ENST00000763589.1:n.248+19678C>T

Variant summary

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

The ENST00000763589.1(ENSG00000299445):​n.248+19678C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0863 in 152,092 control chromosomes in the GnomAD database, including 876 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 0.086 (876 hom., cov: 32)
• Consequence: ENSG00000299445 ENST00000763589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 1 publications found

Genes affected

ENSG00000299445 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763589.1. 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
	ENSG00000299445	ENST00000763589.1		n.248+19678C>T		intron	N/A
	ENSG00000299445	ENST00000763590.1		n.203+19678C>T		intron	N/A
	ENSG00000299445	ENST00000763591.1		n.70-27834C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0861 AC: 13092 AN: 151974 Hom.: 871 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.0447

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0142

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0466

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0863 AC: 13121 AN: 152092 Hom.: 876 Cov.: 32 AF XY: 0.0845 AC XY: 6282 AN XY: 74330

African (AFR) AF: 0.185 AC: 7676 AN: 41474

American (AMR) AF: 0.0555 AC: 848 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3470

East Asian (EAS) AF: 0.0442 AC: 229 AN: 5178

South Asian (SAS) AF: 0.115 AC: 555 AN: 4812

European-Finnish (FIN) AF: 0.0142 AC: 150 AN: 10570

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.0466 AC: 3167 AN: 68000

Other (OTH) AF: 0.0881 AC: 186 AN: 2112

Alfa AF: 0.0329 Hom.: 42

Bravo AF: 0.0916

Asia WGS AF: 0.117 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		0.032

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10484990;

hg19: chr6-54548309;