7-145337519-C-A

Variant names:

• chr7-145337519-C-A
• rs1468375

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;