rs10483636

Variant names:

• chr14-54334127-A-G
• rs10483636
• ENST00000770016.1:n.370-33950T>C

Your query was ambiguous. Multiple possible variants found:

• chr14-54334127-A-G
• chr14-54334127-A-T

Variant summary

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

The ENST00000770016.1(ENSG00000300202):​n.370-33950T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.07 in 152,260 control chromosomes in the GnomAD database, including 748 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 0.070 (748 hom., cov: 33)
• Consequence: ENSG00000300202 ENST00000770016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 4 publications found

Genes affected

ENSG00000300202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770016.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300202	ENST00000770016.1		n.370-33950T>C		intron	N/A
	ENSG00000300202	ENST00000770017.1		n.410-33950T>C		intron	N/A
	ENSG00000300202	ENST00000770018.1		n.522-33950T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0697 AC: 10609 AN: 152142 Hom.: 742 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00786

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0300

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0700 AC: 10652 AN: 152260 Hom.: 748 Cov.: 33 AF XY: 0.0670 AC XY: 4986 AN XY: 74468

African (AFR) AF: 0.178 AC: 7393 AN: 41524

American (AMR) AF: 0.0433 AC: 663 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.00787 AC: 38 AN: 4830

European-Finnish (FIN) AF: 0.0134 AC: 142 AN: 10606

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0300 AC: 2041 AN: 68022

Other (OTH) AF: 0.0545 AC: 115 AN: 2112

Alfa AF: 0.0353 Hom.: 289

Bravo AF: 0.0767

Asia WGS AF: 0.0150 AC: 51 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.70
DANN	Benign	0.59
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs10483636; hg19: chr14-54800845;