rs6705593

Variant names:

• chr2-203906791-C-G
• rs6705593
• ENST00000810800.1:n.204-8498C>G

Your query was ambiguous. Multiple possible variants found:

• chr2-203906791-C-G
• chr2-203906791-C-T

Variant summary

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

The ENST00000810800.1(ENSG00000305408):​n.204-8498C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,830 control chromosomes in the GnomAD database, including 14,855 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 0.44 (14855 hom., cov: 32)
• Consequence: ENSG00000305408 ENST00000810800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314
• Publications: 4 publications found

Genes affected

ENSG00000305408 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810800.1. 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
	ENSG00000305408	ENST00000810800.1		n.204-8498C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66466 AN: 151712 Hom.: 14850 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.438 AC: 66494 AN: 151830 Hom.: 14855 Cov.: 32 AF XY: 0.433 AC XY: 32145 AN XY: 74164

African (AFR) AF: 0.422 AC: 17456 AN: 41372

American (AMR) AF: 0.416 AC: 6349 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1222 AN: 5174

South Asian (SAS) AF: 0.516 AC: 2480 AN: 4802

European-Finnish (FIN) AF: 0.357 AC: 3745 AN: 10492

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31867 AN: 67928

Other (OTH) AF: 0.463 AC: 976 AN: 2108

Alfa AF: 0.308 Hom.: 737

Bravo AF: 0.439

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.1
DANN	Benign	0.30
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs6705593; hg19: chr2-204771514;