rs7202238

Variant names:

• chr16-52355906-T-C
• rs7202238
• ENST00000701553.1:n.193+406A>G

Variant summary

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

The ENST00000701553.1(ENSG00000289907):​n.193+406A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,016 control chromosomes in the GnomAD database, including 11,588 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 0.39 (11588 hom., cov: 33)
• Consequence: ENSG00000289907 ENST00000701553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 0 publications found

Genes affected

ENSG00000289907 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701553.1. 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
	ENSG00000289907	ENST00000701553.1		n.193+406A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58769 AN: 151898 Hom.: 11575 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.387 AC: 58798 AN: 152016 Hom.: 11588 Cov.: 33 AF XY: 0.383 AC XY: 28476 AN XY: 74308

African (AFR) AF: 0.406 AC: 16835 AN: 41440

American (AMR) AF: 0.332 AC: 5064 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1490 AN: 3462

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5184

South Asian (SAS) AF: 0.293 AC: 1409 AN: 4816

European-Finnish (FIN) AF: 0.338 AC: 3575 AN: 10564

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28126 AN: 67966

Other (OTH) AF: 0.410 AC: 865 AN: 2112

Alfa AF: 0.406 Hom.: 6600

Bravo AF: 0.388

Asia WGS AF: 0.249 AC: 867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.9
DANN	Benign	0.72
PhyloP100		0.13

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: rs7202238;

hg19: chr16-52389818;