ENST00000637807.1:c.2373+21175T>C

Variant names:

• chr7-17361403-T-C
• rs7791070
• ENST00000637807.1:c.2373+21175T>C

Variant summary

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

The ENST00000637807.1(ENSG00000283321):​c.2373+21175T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,096 control chromosomes in the GnomAD database, including 8,943 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 0.31 (8943 hom., cov: 32)
• Consequence: ENSG00000283321 ENST00000637807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 3 publications found

Genes affected

ENSG00000283321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283321	ENST00000637807.1	c.2373+21175T>C		intron_variant	Intron 10 of 11	5		ENSP00000490530.1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47758 AN: 151978 Hom.: 8903 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.315 AC: 47855 AN: 152096 Hom.: 8943 Cov.: 32 AF XY: 0.313 AC XY: 23287 AN XY: 74344

African (AFR) AF: 0.512 AC: 21220 AN: 41446

American (AMR) AF: 0.343 AC: 5242 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3468

East Asian (EAS) AF: 0.389 AC: 2012 AN: 5166

South Asian (SAS) AF: 0.266 AC: 1285 AN: 4824

European-Finnish (FIN) AF: 0.177 AC: 1875 AN: 10588

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14742 AN: 67988

Other (OTH) AF: 0.291 AC: 614 AN: 2112

Alfa AF: 0.242 Hom.: 2585

Bravo AF: 0.339

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.83
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7791070; hg19: chr7-17401027;