rs13222675

Variant names:

• chr7-86282105-T-C
• rs13222675
• ENST00000757672.1:n.92+6663A>G

Variant summary

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

The ENST00000757672.1(ENSG00000298738):​n.92+6663A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 152,236 control chromosomes in the GnomAD database, including 503 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 0.068 (503 hom., cov: 32)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599
• Publications: 1 publications found

Genes affected

ENSG00000298738 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 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
ENSG00000298738	ENST00000757672.1	n.92+6663A>G		intron_variant	Intron 1 of 3
ENSG00000298738	ENST00000757673.1	n.91+6663A>G		intron_variant	Intron 1 of 2
ENSG00000298738	ENST00000757674.1	n.91+6663A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0683 AC: 10388 AN: 152118 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.0674

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0682 AC: 10387 AN: 152236 Hom.: 503 Cov.: 32 AF XY: 0.0676 AC XY: 5035 AN XY: 74448

African (AFR) AF: 0.0176 AC: 732 AN: 41556

American (AMR) AF: 0.0359 AC: 549 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0674 AC: 234 AN: 3472

East Asian (EAS) AF: 0.000581 AC: 3 AN: 5166

South Asian (SAS) AF: 0.0238 AC: 115 AN: 4826

European-Finnish (FIN) AF: 0.138 AC: 1460 AN: 10610

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7068 AN: 67984

Other (OTH) AF: 0.0572 AC: 121 AN: 2114

Alfa AF: 0.0901 Hom.: 371

Bravo AF: 0.0592

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.1
DANN	Benign	0.87
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs13222675; hg19: chr7-85911421;