chr2-200907075-A-G

Variant names:

• chr2-200907075-A-G
• rs13416500
• ENST00000831870.1:n.222-2762T>C

Variant summary

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

The ENST00000831870.1(ENSG00000308129):​n.222-2762T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 148,168 control chromosomes in the GnomAD database, including 4,611 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 0.23 (4611 hom., cov: 30)
• Consequence: ENSG00000308129 ENST00000831870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 6 publications found

Genes affected

ENSG00000308129 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000831870.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308129	ENST00000831870.1		n.222-2762T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 34324 AN: 148036 Hom.: 4603 Cov.: 30

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.00928

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.232 AC: 34374 AN: 148168 Hom.: 4611 Cov.: 30 AF XY: 0.227 AC XY: 16461 AN XY: 72480

African (AFR) AF: 0.381 AC: 15397 AN: 40438

American (AMR) AF: 0.173 AC: 2575 AN: 14918

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 827 AN: 3418

East Asian (EAS) AF: 0.00930 AC: 44 AN: 4730

South Asian (SAS) AF: 0.0837 AC: 388 AN: 4638

European-Finnish (FIN) AF: 0.185 AC: 1889 AN: 10230

Middle Eastern (MID) AF: 0.157 AC: 38 AN: 242

European-Non Finnish (NFE) AF: 0.189 AC: 12595 AN: 66626

Other (OTH) AF: 0.223 AC: 458 AN: 2050

Alfa AF: 0.217 Hom.: 524

Bravo AF: 0.236

Asia WGS AF: 0.0730 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.4
DANN	Benign	0.83
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs13416500; hg19: chr2-201771798;