rs12699472

Variant names:

• chr7-13279871-A-G
• rs12699472
• ENST00000411542.1:n.237-30338A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-13279871-A-G
• chr7-13279871-A-T

Variant summary

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

The ENST00000411542.1(ENSG00000229618):​n.237-30338A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,752 control chromosomes in the GnomAD database, including 5,166 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 0.25 (5166 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 1 publications found

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411542.1. 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
	ENSG00000229618	ENST00000411542.1	TSL:4	n.237-30338A>G		intron	N/A
	ENSG00000229618	ENST00000638964.1	TSL:5	n.609-30338A>G		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.608-30338A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38633 AN: 151636 Hom.: 5159 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.0855

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.255 AC: 38670 AN: 151752 Hom.: 5166 Cov.: 32 AF XY: 0.252 AC XY: 18699 AN XY: 74142

African (AFR) AF: 0.309 AC: 12805 AN: 41404

American (AMR) AF: 0.210 AC: 3193 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3470

East Asian (EAS) AF: 0.0855 AC: 443 AN: 5180

South Asian (SAS) AF: 0.182 AC: 880 AN: 4822

European-Finnish (FIN) AF: 0.261 AC: 2740 AN: 10516

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16823 AN: 67838

Other (OTH) AF: 0.259 AC: 544 AN: 2104

Alfa AF: 0.250 Hom.: 2794

Bravo AF: 0.254

Asia WGS AF: 0.165 AC: 570 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.20
DANN	Benign	0.56
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs12699472; hg19: chr7-13319496;