7-13319569-C-G

Variant names:

• chr7-13319569-C-G
• rs4721214
• ENST00000411542.1:n.351+9246C>G

Variant summary

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

The ENST00000411542.1(ENSG00000229618):​n.351+9246C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 151,570 control chromosomes in the GnomAD database, including 41,284 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 0.73 (41284 hom., cov: 29)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 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

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
	ENSG00000229618	ENST00000411542.1	TSL:4	n.351+9246C>G		intron	N/A
	ENSG00000229618	ENST00000638964.1	TSL:5	n.723+9246C>G		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.722+9246C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.732 AC: 110881 AN: 151456 Hom.: 41228 Cov.: 29

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.732 AC: 111005 AN: 151570 Hom.: 41284 Cov.: 29 AF XY: 0.726 AC XY: 53788 AN XY: 74056

African (AFR) AF: 0.827 AC: 34241 AN: 41392

American (AMR) AF: 0.713 AC: 10812 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2384 AN: 3464

East Asian (EAS) AF: 0.375 AC: 1914 AN: 5106

South Asian (SAS) AF: 0.646 AC: 3100 AN: 4800

European-Finnish (FIN) AF: 0.690 AC: 7254 AN: 10508

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48840 AN: 67810

Other (OTH) AF: 0.711 AC: 1502 AN: 2112

Alfa AF: 0.617 Hom.: 1652

Bravo AF: 0.739

Asia WGS AF: 0.561 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.69
DANN	Benign	0.46
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4721214; hg19: chr7-13359194;