chr7-17364072-G-A

Variant names:

• chr7-17364072-G-A
• rs10274243
• ENST00000637807.1:c.2373+23844G>A

Variant summary

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

The ENST00000637807.1(ENSG00000283321):​c.2373+23844G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,064 control chromosomes in the GnomAD database, including 3,034 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 0.17 (3034 hom., cov: 32)
• Consequence: ENSG00000283321 ENST00000637807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375171	XR_927074.3	n.212+244C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283321	ENST00000637807.1	c.2373+23844G>A		intron_variant	Intron 10 of 11	5		ENSP00000490530.1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26390 AN: 151946 Hom.: 3023 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.174 AC: 26440 AN: 152064 Hom.: 3034 Cov.: 32 AF XY: 0.174 AC XY: 12972 AN XY: 74342

African (AFR) AF: 0.307 AC: 12719 AN: 41460

American (AMR) AF: 0.137 AC: 2097 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1977 AN: 5172

South Asian (SAS) AF: 0.158 AC: 760 AN: 4818

European-Finnish (FIN) AF: 0.106 AC: 1116 AN: 10566

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6885 AN: 67986

Other (OTH) AF: 0.145 AC: 307 AN: 2110

Alfa AF: 0.119 Hom.: 1506

Bravo AF: 0.183

Asia WGS AF: 0.231 AC: 800 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.034
DANN	Benign	0.45
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10274243; hg19: chr7-17403696;