chr7-99161494-C-A

Position:

• chr7-99161494-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017012211.2(KPNA7):​c.1546-15178G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,014 control chromosomes in the GnomAD database, including 35,431 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 0.67 (35431 hom., cov: 32)
• Consequence: KPNA7 XM_017012211.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950

Genes affected

KPNA7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KPNA7	XM_017012211.2	c.1546-15178G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102000 AN: 151896 Hom.: 35411 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.671 AC: 102067 AN: 152014 Hom.: 35431 Cov.: 32 AF XY: 0.675 AC XY: 50181 AN XY: 74300

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.657

Alfa AF: 0.724 Hom.: 81432

Bravo AF: 0.662

Asia WGS AF: 0.708 AC: 2465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9297145; hg19: chr7-98759117;