rs1866206

Variant names:

• chr2-60639691-G-A
• rs1866206
• ENST00000731138.1:n.440C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-60639691-G-A
• chr2-60639691-G-C

Variant summary

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

The ENST00000731138.1(ENSG00000295595):​n.440C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,056 control chromosomes in the GnomAD database, including 10,579 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 (10579 hom., cov: 33)
• Consequence: ENSG00000295595 ENST00000731138.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 2 publications found

Genes affected

ENSG00000295595 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731138.1. 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
	ENSG00000295595	ENST00000731138.1		n.440C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54059 AN: 151938 Hom.: 10549 Cov.: 33

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.356 AC: 54136 AN: 152056 Hom.: 10579 Cov.: 33 AF XY: 0.349 AC XY: 25960 AN XY: 74312

African (AFR) AF: 0.521 AC: 21604 AN: 41486

American (AMR) AF: 0.329 AC: 5020 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 954 AN: 3470

East Asian (EAS) AF: 0.110 AC: 572 AN: 5184

South Asian (SAS) AF: 0.193 AC: 929 AN: 4816

European-Finnish (FIN) AF: 0.296 AC: 3119 AN: 10544

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20911 AN: 67968

Other (OTH) AF: 0.327 AC: 689 AN: 2110

Alfa AF: 0.317 Hom.: 4119

Bravo AF: 0.367

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.90
DANN	Benign	0.54
PhyloP100		-0.27

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: rs1866206;

hg19: chr2-60866826;