rs13414200

Variant names:

• chr2-13374171-G-A
• rs13414200
• ENST00000772676.1:n.77+16818G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-13374171-G-A
• chr2-13374171-G-T

Variant summary

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

The ENST00000772676.1(ENSG00000300555):​n.77+16818G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 151,186 control chromosomes in the GnomAD database, including 1,922 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 0.15 (1922 hom., cov: 32)
• Consequence: ENSG00000300555 ENST00000772676.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 2 publications found

Genes affected

ENSG00000300555 (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 (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772676.1. 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
	ENSG00000300555	ENST00000772676.1		n.77+16818G>A		intron	N/A
	ENSG00000300555	ENST00000772677.1		n.78-12951G>A		intron	N/A
	ENSG00000300555	ENST00000772678.1		n.76+16818G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22804 AN: 151072 Hom.: 1921 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.151 AC: 22836 AN: 151186 Hom.: 1922 Cov.: 32 AF XY: 0.155 AC XY: 11427 AN XY: 73874

African (AFR) AF: 0.196 AC: 8115 AN: 41362

American (AMR) AF: 0.189 AC: 2851 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 623 AN: 3452

East Asian (EAS) AF: 0.247 AC: 1271 AN: 5140

South Asian (SAS) AF: 0.175 AC: 842 AN: 4812

European-Finnish (FIN) AF: 0.127 AC: 1340 AN: 10524

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7362 AN: 67472

Other (OTH) AF: 0.146 AC: 307 AN: 2100

Alfa AF: 0.134 Hom.: 226

Bravo AF: 0.159

Asia WGS AF: 0.186 AC: 644 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.30
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13414200; hg19: chr2-13514296;