rs2475803

Variant names:

• chr6-39964255-C-A
• rs2475803
• ENST00000649703.2:n.210+15752C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-39964255-C-A
• chr6-39964255-C-T

Variant summary

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

The ENST00000649703.2(ENSG00000293066):​n.210+15752C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,106 control chromosomes in the GnomAD database, including 10,925 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 0.36 (10925 hom., cov: 33)
• Consequence: ENSG00000293066 ENST00000649703.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 3 publications found

Genes affected

ENSG00000293066 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649703.2. 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
	ENSG00000293066	ENST00000649703.2		n.210+15752C>A		intron	N/A
	ENSG00000293066	ENST00000741538.1		n.256+15752C>A		intron	N/A
	ENSG00000293066	ENST00000741539.1		n.153+696C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54414 AN: 151988 Hom.: 10919 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.358 AC: 54423 AN: 152106 Hom.: 10925 Cov.: 33 AF XY: 0.364 AC XY: 27083 AN XY: 74360

African (AFR) AF: 0.161 AC: 6676 AN: 41514

American (AMR) AF: 0.491 AC: 7505 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1604 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1982 AN: 5168

South Asian (SAS) AF: 0.511 AC: 2461 AN: 4820

European-Finnish (FIN) AF: 0.456 AC: 4822 AN: 10574

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27843 AN: 67958

Other (OTH) AF: 0.380 AC: 803 AN: 2112

Alfa AF: 0.309 Hom.: 1311

Bravo AF: 0.350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.74
PhyloP100		-1.0

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: rs2475803;

hg19: chr6-39931994;