rs1468375

chr7-145337519-C-Achr7-145337519-C-T

Variant summary

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

The variant allele was found at a frequency of 0.402 in 151,914 control chromosomes in the GnomAD database, including 12,782 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 0.40 (12782 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61002 AN: 151796 Hom.: 12774 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.402 AC: 61047 AN: 151914 Hom.: 12782 Cov.: 31 AF XY: 0.399 AC XY: 29588 AN XY: 74214

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.429

Alfa AF: 0.416 Hom.: 7627

Bravo AF: 0.397

Asia WGS AF: 0.260 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.20
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468375; hg19: chr7-145034612;