rs10484990

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-54683511-G-A
• chr6-54683511-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986606	XR_001744176.3	n.96-27834C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299445	ENST00000763589.1	n.248+19678C>T		intron_variant	Intron 2 of 6
ENSG00000299445	ENST00000763590.1	n.203+19678C>T		intron_variant	Intron 2 of 5
ENSG00000299445	ENST00000763591.1	n.70-27834C>T		intron_variant	Intron 1 of 4
ENSG00000299445	ENST00000763592.1	n.196+19678C>T		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs10484990; hg19: chr6-54548309;