rs16212

Variant names:

• chr7-24225042-C-G
• rs16212
• ENST00000439839.1:n.160-28013G>C

Variant summary

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

The ENST00000718234.1(ENSG00000228944):​n.320-28013G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 152,238 control chromosomes in the GnomAD database, including 295 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 0.056 (295 hom., cov: 32)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 3 publications found

Genes affected

ENSG00000228944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718234.1. 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
	ENSG00000228944	ENST00000439839.1	TSL:5	n.160-28013G>C		intron	N/A
	ENSG00000228944	ENST00000718234.1		n.320-28013G>C		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.342-28013G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0564 AC: 8572 AN: 152120 Hom.: 293 Cov.: 32

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0372

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0564 AC: 8586 AN: 152238 Hom.: 295 Cov.: 32 AF XY: 0.0561 AC XY: 4176 AN XY: 74442

African (AFR) AF: 0.0893 AC: 3708 AN: 41540

American (AMR) AF: 0.0572 AC: 875 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3470

East Asian (EAS) AF: 0.141 AC: 729 AN: 5178

South Asian (SAS) AF: 0.0485 AC: 234 AN: 4822

European-Finnish (FIN) AF: 0.0268 AC: 284 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0372 AC: 2532 AN: 68014

Other (OTH) AF: 0.0531 AC: 112 AN: 2110

Alfa AF: 0.0488 Hom.: 20

Bravo AF: 0.0607

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	10
DANN	Benign	0.55
PhyloP100		0.14

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: rs16212;

hg19: chr7-24264661;