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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984901	XR_001752184.1	n.279+406A>G		intron_variant	Intron 2 of 5
LOC107984901	XR_001752185.2	n.193+406A>G		intron_variant	Intron 2 of 5
LOC107984901	XR_001752186.1	n.279+406A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289907	ENST00000701553.1	n.193+406A>G		intron_variant	Intron 2 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs7202238; hg19: chr16-52389818;